atoms moving after FIT_TO_TEMPLATE
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Vojtech Spiwok
Aug 10, 2017, 4:28:15 AM8/10/17
to PLUMED users
Ciao a tutti,
I'm trying to use FIT_TO_TEMPLATE. I had some strange results so I tried
a 10-step MD in Gromacs/Plumed with printing of coordinates in every step:
WHOLEMOLECULES ENTITY0=1-22
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=after_mtd1_1noh.pdb TYPE=OPTIMAL
a1: POSITION ATOM=1
a2: POSITION ATOM=5
etc
PRINT ARG=a1.x,a1.y,a1.z,a2.x,a2.y,a2.z,etc STRIDE=1 FILE=COLVAR
(etc replaces other atoms)
When I did DUMPATOMS before and after FIT_TO_TEMPLATE the output xyz files
were correct. But coordinates in COLVAR are strange. First, they are somehow
broken by PBC (despite the fact that the molecule is not broken during the MD).
I took these coordinates and reconstructed PBC, so I got whole molecule in PDB
format. Unfortunately, these molecules move translationally despite being
fitted to the template.
I tried plumed 2.3 and 2.4a, with and without MPI, but no success.
I also tried SCALED_COMPONENTS, which changes the situation with PBC but not
with fitting.
Some suggestions? Many thanks!
Vojtech Spiwok
I'm trying to use FIT_TO_TEMPLATE. I had some strange results so I tried
a 10-step MD in Gromacs/Plumed with printing of coordinates in every step:
WHOLEMOLECULES ENTITY0=1-22
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=after_mtd1_1noh.pdb TYPE=OPTIMAL
a1: POSITION ATOM=1
a2: POSITION ATOM=5
etc
PRINT ARG=a1.x,a1.y,a1.z,a2.x,a2.y,a2.z,etc STRIDE=1 FILE=COLVAR
(etc replaces other atoms)
When I did DUMPATOMS before and after FIT_TO_TEMPLATE the output xyz files
were correct. But coordinates in COLVAR are strange. First, they are somehow
broken by PBC (despite the fact that the molecule is not broken during the MD).
I took these coordinates and reconstructed PBC, so I got whole molecule in PDB
format. Unfortunately, these molecules move translationally despite being
fitted to the template.
I tried plumed 2.3 and 2.4a, with and without MPI, but no success.
I also tried SCALED_COMPONENTS, which changes the situation with PBC but not
with fitting.
Some suggestions? Many thanks!
Vojtech Spiwok
Giovanni Bussi
Aug 12, 2017, 3:38:45 PM8/12/17
to plumed...@googlegroups.com
Can you try POSITION NOPBC?
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Spiwok Vojtech
Aug 13, 2017, 11:43:50 AM8/13/17
to plumed...@googlegroups.com
Ciao,
I will!
Vojtech
________________________________
From: plumed...@googlegroups.com <plumed...@googlegroups.com> on behalf of Giovanni Bussi <giovann...@gmail.com>
Sent: 12 August 2017 21:38:32
To: plumed...@googlegroups.com
Subject: Re: [plumed-users] atoms moving after FIT_TO_TEMPLATE
Can you try POSITION NOPBC?
To post to this group, send email to plumed...@googlegroups.com<mailto:plumed...@googlegroups.com>.
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I will!
Vojtech
________________________________
From: plumed...@googlegroups.com <plumed...@googlegroups.com> on behalf of Giovanni Bussi <giovann...@gmail.com>
Sent: 12 August 2017 21:38:32
To: plumed...@googlegroups.com
Subject: Re: [plumed-users] atoms moving after FIT_TO_TEMPLATE
Can you try POSITION NOPBC?
Il giorno gio 10 ago 2017 alle 10:28 Vojtech Spiwok <spi...@vscht.cz<mailto:spi...@vscht.cz>> ha scritto:
Ciao a tutti,
I'm trying to use FIT_TO_TEMPLATE. I had some strange results so I tried
a 10-step MD in Gromacs/Plumed with printing of coordinates in every step:
WHOLEMOLECULES ENTITY0=1-22
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=after_mtd1_1noh.pdb TYPE=OPTIMAL
a1: POSITION ATOM=1
a2: POSITION ATOM=5
etc
PRINT ARG=a1.x,a1.y,a1.z,a2.x,a2.y,a2.z,etc STRIDE=1 FILE=COLVAR
(etc replaces other atoms)
When I did DUMPATOMS before and after FIT_TO_TEMPLATE the output xyz files
were correct. But coordinates in COLVAR are strange. First, they are somehow
broken by PBC (despite the fact that the molecule is not broken during the MD).
I took these coordinates and reconstructed PBC, so I got whole molecule in PDB
format. Unfortunately, these molecules move translationally despite being
fitted to the template.
I tried plumed 2.3 and 2.4a, with and without MPI, but no success.
I also tried SCALED_COMPONENTS, which changes the situation with PBC but not
with fitting.
Some suggestions? Many thanks!
Vojtech Spiwok
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Ciao a tutti,
I'm trying to use FIT_TO_TEMPLATE. I had some strange results so I tried
a 10-step MD in Gromacs/Plumed with printing of coordinates in every step:
WHOLEMOLECULES ENTITY0=1-22
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=after_mtd1_1noh.pdb TYPE=OPTIMAL
a1: POSITION ATOM=1
a2: POSITION ATOM=5
etc
PRINT ARG=a1.x,a1.y,a1.z,a2.x,a2.y,a2.z,etc STRIDE=1 FILE=COLVAR
(etc replaces other atoms)
When I did DUMPATOMS before and after FIT_TO_TEMPLATE the output xyz files
were correct. But coordinates in COLVAR are strange. First, they are somehow
broken by PBC (despite the fact that the molecule is not broken during the MD).
I took these coordinates and reconstructed PBC, so I got whole molecule in PDB
format. Unfortunately, these molecules move translationally despite being
fitted to the template.
I tried plumed 2.3 and 2.4a, with and without MPI, but no success.
I also tried SCALED_COMPONENTS, which changes the situation with PBC but not
with fitting.
Some suggestions? Many thanks!
Vojtech Spiwok
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Vojtech Spiwok
Aug 13, 2017, 3:26:22 PM8/13/17
to PLUMED users
Yes!
POSITION NOPBC is the key!
It works well even though the molecule jumps across PBC.
I owe you absinthe!
Vojtech
POSITION NOPBC is the key!
It works well even though the molecule jumps across PBC.
I owe you absinthe!
Vojtech
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