Groups
Sign in
Groups
browndye-users-l
Conversations
About
Send feedback
Help
browndye-users-l
Contact owners and managers
1–30 of 35
Mark all as read
Report group
0 selected
Lane Votapka
2
May 18
Should non ATOM or HETATM lines be ignored in pqr2xml
Aha! I did find a way to instruct parmed to leave out the CRYST line. For future reference, for the
unread,
Should non ATOM or HETATM lines be ignored in pqr2xml
Aha! I did find a way to instruct parmed to leave out the CRYST line. For future reference, for the
May 18
Gary Huber
12/29/23
new release
Dear Browndye users, A new release is out that fixes a bug in the constraint satisfier. If your
unread,
new release
Dear Browndye users, A new release is out that fixes a bug in the constraint satisfier. If your
12/29/23
Conor Abraham
,
Gary Huber
3
11/3/23
Atom indexing question
Hi Gary, Thank you so much! Best, Conor On Friday, November 3, 2023 at 4:13:30 PM UTC-4 gahu...@gmail
unread,
Atom indexing question
Hi Gary, Thank you so much! Best, Conor On Friday, November 3, 2023 at 4:13:30 PM UTC-4 gahu...@gmail
11/3/23
Gary Huber
10/19/23
new release
Dear Browndye users, I've fixed a bug that was sometimes causing born_integral to crash when
unread,
new release
Dear Browndye users, I've fixed a bug that was sometimes causing born_integral to crash when
10/19/23
Benjamin Hall
,
Gary Huber
3
10/7/23
Segfault Win11/WSL/Ubuntu 22.04
Hi Gary I repeated the tutorial with the release from yesterday and I no longer see the segfault.
unread,
Segfault Win11/WSL/Ubuntu 22.04
Hi Gary I repeated the tutorial with the release from yesterday and I no longer see the segfault.
10/7/23
Gary Huber
10/6/23
new release
Dear Browndye Users, A new release is out. First of all, there have been some difficulties with
unread,
new release
Dear Browndye Users, A new release is out. First of all, there have been some difficulties with
10/6/23
Conor Abraham
8/14/23
Question about Coplanar Constraints and Improper Dihedral Angles
Hi Gary, I have been trying to apply the CHARMM46 forcefield in Browndye, but am hitting a roadblock
unread,
Question about Coplanar Constraints and Improper Dihedral Angles
Hi Gary, I have been trying to apply the CHARMM46 forcefield in Browndye, but am hitting a roadblock
8/14/23
Conor Abraham
,
Gary Huber
3
8/8/23
Question about units and two simulation file parameters
Hi Gary, No problem on the delay. Thanks so much for your help! Best, Conor On Monday, August 7, 2023
unread,
Question about units and two simulation file parameters
Hi Gary, No problem on the delay. Thanks so much for your help! Best, Conor On Monday, August 7, 2023
8/8/23
Lane Votapka
, …
Robert Konecny
4
7/31/23
Problem with latest APBS version and make_apbs_inputs
Hi All, Ah yes, that makes sense, Robert. Also, Gary, I realized what the problem was - I had been
unread,
Problem with latest APBS version and make_apbs_inputs
Hi All, Ah yes, that makes sense, Robert. Also, Gary, I realized what the problem was - I had been
7/31/23
Sunil Tripathi
, …
Lane Votapka
4
6/21/23
Computing Rate constant-Reg.
Dear Gary and Lane, Thank you both for your valuable suggestions. I will go ahead accordingly. Best
unread,
Computing Rate constant-Reg.
Dear Gary and Lane, Thank you both for your valuable suggestions. I will go ahead accordingly. Best
6/21/23
Gary Huber
6/14/23
new release
Dear Browndye users, The latest release fixes a bug in born_integral that could cause a crash if the
unread,
new release
Dear Browndye users, The latest release fixes a bug in born_integral that could cause a crash if the
6/14/23
Gary Huber
4/28/23
additional thanks
Hi, again, folks, I forgot to thank also Abraham Muñiz Chicharro from the Wade group for helping with
unread,
additional thanks
Hi, again, folks, I forgot to thank also Abraham Muñiz Chicharro from the Wade group for helping with
4/28/23
Gary Huber
4/28/23
New Browndye release
Dear Users, A new release is now on the website. I have added a new option to the born_integral
unread,
New Browndye release
Dear Users, A new release is now on the website. I have added a new option to the born_integral
4/28/23
Bruce Niessner
,
Gary Huber
4
4/17/23
non-polar desolvation forces
Correct; we do not have a separate exclusion grid like SDA. It's all done through the LJ forces.
unread,
non-polar desolvation forces
Correct; we do not have a separate exclusion grid like SDA. It's all done through the LJ forces.
4/17/23
Bruce Niessner
,
Gary Huber
2
4/13/23
Visualising trajectories
Hi, Jakob, Yes, I recently got rid of the -traj option and now the trajectory.xml file comes in
unread,
Visualising trajectories
Hi, Jakob, Yes, I recently got rid of the -traj option and now the trajectory.xml file comes in
4/13/23
Gary Huber
1/25/23
bug fix
Dear Browndye users, I have fixed a bug that was causing some weighted-ensemble simulations to crash.
unread,
bug fix
Dear Browndye users, I have fixed a bug that was causing some weighted-ensemble simulations to crash.
1/25/23
Gary Huber
1/24/23
new Browndye release
Dear Browndye users, A new release is available, fixing bugs that caused it to freeze for the case of
unread,
new Browndye release
Dear Browndye users, A new release is available, fixing bugs that caused it to freeze for the case of
1/24/23
Pulkit A Sati
12/22/22
error while running browndye2 job
Dear Browndye developers, We (myself and @https://github.com/vaibhavadixit) have been attempting to
unread,
error while running browndye2 job
Dear Browndye developers, We (myself and @https://github.com/vaibhavadixit) have been attempting to
12/22/22
Pulkit A Sati
,
Lane Votapka
2
12/13/22
installtion of browndye2 in conda env
Hi, I do this frequently, but most of the dependencies need to be installed independently from the
unread,
installtion of browndye2 in conda env
Hi, I do this frequently, but most of the dependencies need to be installed independently from the
12/13/22
Gary Huber
12/9/22
new release for Browndye
Dear Browndye users, We have released a new version, the first since this summer. Here's a
unread,
new release for Browndye
Dear Browndye users, We have released a new version, the first since this summer. Here's a
12/9/22
Gary Huber
6/13/22
New Browndye Release
Dear Browndye Users, Our new release fixes a bug that was causing build_bins to crash for the
unread,
New Browndye Release
Dear Browndye Users, Our new release fixes a bug that was causing build_bins to crash for the
6/13/22
Gary Huber
5/18/22
new Browndye release
Dear Browndye users, We released a new version, fixing a bug in bd_top. This might affect you if you
unread,
new Browndye release
Dear Browndye users, We released a new version, fixing a bug in bd_top. This might affect you if you
5/18/22
Lane Votapka
4/25/22
Question about viscosity and permittivity units
Hi Gary, I'm looking at the results.xml file, trying to use Browndye 2 to recreate a Smoluchowski
unread,
Question about viscosity and permittivity units
Hi Gary, I'm looking at the results.xml file, trying to use Browndye 2 to recreate a Smoluchowski
4/25/22
Gerald Keller
,
Robert Konecny
7
4/19/22
compiling browndye 2 on HPC
Hi Gerald, Good to hear you were able to finish the compilation! It's interesting that your
unread,
compiling browndye 2 on HPC
Hi Gerald, Good to hear you were able to finish the compilation! It's interesting that your
4/19/22
Gary Huber
3/7/22
new Browndye release
Dear Browndye users, I have posted a new release of Browndye 2. Most importantly, this fixed a bug
unread,
new Browndye release
Dear Browndye users, I have posted a new release of Browndye 2. Most importantly, this fixed a bug
3/7/22
Lane Votapka
,
Robert Konecny
3
2/11/22
Browndye2 for Ubuntu 18
Thanks for the suggestion Gerald, and thank you Robert for the link, that seemed to work well. Lane
unread,
Browndye2 for Ubuntu 18
Thanks for the suggestion Gerald, and thank you Robert for the link, that seemed to work well. Lane
2/11/22
Gary Huber
1/26/22
new release
Dear Browndye users, We have a new release. A new feature is the ability to define a "restraint
unread,
new release
Dear Browndye users, We have a new release. A new feature is the ability to define a "restraint
1/26/22
Gary Huber
1/12/22
new release
Dear Browndye users, The latest release fixes some bugs I found while doing a simulation of a
unread,
new release
Dear Browndye users, The latest release fixes some bugs I found while doing a simulation of a
1/12/22
Gary Huber
1/4/22
new Browndye release
Dear Browndye Users, We have a new release. Among other things, this release includes the ability to
unread,
new Browndye release
Dear Browndye Users, We have a new release. Among other things, this release includes the ability to
1/4/22
Gary Huber
12/14/21
new release
Dear Browndye users, I've just fixed a bug, introduced with the recent constant time step option,
unread,
new release
Dear Browndye users, I've just fixed a bug, introduced with the recent constant time step option,
12/14/21