CMAP scaling with CHARMM36m force field for REST2 simulations

[chev1...@gmail.com]

Dear All,

I am setting up REST2 simulations with charmm36m ff using plumed2-2.7.0 patched to Gromacs 2020.4. 

I went through the previous posts on scaling CMAP section and there is a script provided by Riccardo. Further,  Chris suggests few fixes to the script and there is a follow up reply from Giovanni that the changes will be integrated to the partial_tempering script.

Please can I know if I still need to use the original script from Riccardo or use the version with fixes suggested from Chris or are these already integrated into the partial_tempering script and not requiring to run the script from Riccardo.

Kind Regards,

Chetan

[Giovanni Bussi]

Hi,

I think it has not been implemented.

Giovanni

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[chev1...@gmail.com]

Dear Giovanni,

Thanks. I checked the topology files with and without running the script from Riccardo. The CMAP is scaled only after running the script provided in the forum.

I have  couple of  question on pairtypes section.

1) The pairtypes are scaled without the script as well, but after using the script there seems to be some repeats. Is it suppose to

be like this ? Below are few lines from pairtype section:

##without Riccardo's script

[ pairtypes ]
; i     j       func    sigma1-4        epsilon1-4
H H 1 4.00013524445e-02 1.92464000000e-01
H_ H 1 0.0400014 0.136093  ; scaled
H H_ 1 0.0400014 0.136093  ; scaled
H_ H_ 1 0.0400014 0.096232  ; scaled

##with Riccardo's script

[ pairtypes ]
; i     j       func    sigma1-4        epsilon1-4
;_      i       0       0.000000000000  0.000000000000    ; scaled
;       i_      0       0.000000000000  0.000000000000    ; scaled
H H 1 4.00013524445e-02 1.92464000000e-01
H_      H_      1       0.040001352445  0.096232000000   ; scaled
H_      H       1       0.040001352445  0.136092599534    ; scaled
H       H_      1       0.040001352445  0.136092599534    ; scaled
H_ H 1 0.0400014 0.136093  ; scaled
H_      H_      1       0.040001400000  0.068046500000   ; scaled
H__     H       1       0.040001400000  0.096232283172    ; scaled
H_      H_      1       0.040001400000  0.096232283172    ; scaled
H H_ 1 0.0400014 0.136093  ; scaled
H_      H__     1       0.040001400000  0.068046500000   ; scaled
H_      H_      1       0.040001400000  0.096232283172    ; scaled
H       H__     1       0.040001400000  0.096232283172    ; scaled
H_ H_ 1 0.0400014 0.096232  ; scaled
H__     H__     1       0.040001400000  0.048116000000   ; scaled
H__     H_      1       0.040001400000  0.068046299767    ; scaled
H_      H__     1       0.040001400000  0.068046299767    ; scaled

2) with Riccardo's script there are atoms in [pairtypes] with 2 underscore signs  "H__" which is missing in the [atomtypes section] since it is "H_". The grompp steps fails with below error:

ERROR 1 [file scaled_topol.top, line 280]:
  Atomtype H__ not found

I understand the error message, but not sure why the script adds two underscore signs next to the atom "H__".

Kind  Regards,

Chetan

[Giovanni Bussi]

Mm on this perhaps the author of the script could answer better than me... I actually never used charmm. Giovanni

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[RXG]

Dear Chetan:

It has been a while, but I just had the same problem using Riccardo's script to correct cmap terms in REST2.

I am wondering how you fix the problem, i.e., the atoms in the pairtypes with two underscore are not included in the atomtypes? do we need to add that part to the top file or what?

Sorry to disturbe, and any suggestions are highly appreciate.

Cheers,

Ruoxu Gu