Re: [gmx-users] Lost particles while sorting

Will upload to dropbox later (strict 'no external cloud' institutional policy). I don't know if the tpr is completely self-contained, so please let me know if you need the ff folder as well. Thank you, Alex On Wed, Nov 1, 2017 at 4:42 PM, Mark Abraham wrote: > Hi, >

Re: [gmx-users] Lost particles while sorting

Hi, We have had several reports of "lost particles while sorting" but we would like a .tpr on an issue on redmine.gromacs.org to be able to investigate, please! Mark On Wed, Nov 1, 2017 at 10:19 PM Alex wrote: > Hi all, > > I am using walls in the cowboy mode, GMX v.

[gmx-users] Lost particles while sorting

Hi all, I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous membrane (periodic in XY) with water and ions -- everything works fine with pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency error: Lost particles while sorting." mdp exerpt below: pbc

[gmx-users] Problem using gmx wham

Hi, I am attempting to use gmx wham to compute a potential of mean force. I have used the command line: gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ where tpr-files.dat and pullf-files.dat contain a list of the .tpr and pullf.xvg files from each umbrella sampling window,

Re: [gmx-users] Problem on continuing MD

Dear Mark, Thank you so much. I have read the linked website you told and know why such problem happens. Best regards, Ouyang At 2017-11-01 17:39:17, "Mark Abraham" wrote: >Hi, > >See http://www.gromacs.org/Documentation/Terminology/Reproducibility. You

Re: [gmx-users] Problem on continuing MD

Hi, See http://www.gromacs.org/Documentation/Terminology/Reproducibility. You have non-reproducible load balancing. However this is not a problem unless your experimental design hinges upon being able to reproduce an exact trajectory (in which case you will have a tough time getting performance).

[gmx-users] Problem on continuing MD

Dear gromacs user, Today, I continue the MD twice in two directories from the same point of the MD trajectory, for example 100ns, using the same CPU, same checkpoint file, same serve node. To my surprise, the energy informations are different between the two continued log ouput files,

Re: [gmx-users] Amino Acids

Hi, Please try to keep to one email per question :-) Did you read the paper to learn what termini they used? Mark On Wed, 1 Nov 2017 07:34 rose rahmani wrote: > Hi > > If standalone amino acids are zwitterionic and inappropriate for AMBER and > GROMACS ,what do you

[gmx-users] Amino Acids

Hi If standalone amino acids are zwitterionic and inappropriate for AMBER and GROMACS ,what do you think about this article?! Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations *Article* in The Journal of Chemical Physics

[gmx-users] Amino Acids

Hi If standalone amino acids are zwitterionic and inappropriate for AMBER and GROMACS ,what do you think about this article?! Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations *Article* in The Journal of Chemical Physics

[gmx-users] Amino Acids

Hi If standalone amino acids are zwitterionic and inappropriate for AMBER and GROMACS ,what do you think about this article?! Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations *Article* in The Journal of Chemical Physics

[gmx-users] Fwd: Amino acids

-- Forwarded message -- From: Rose Date: Wed, Nov 1, 2017 at 1:06 AM Subject: Amino acids To: Gromacs Hi If standalone amino acids are zwitterionic and inappropriate for AMBER and GROMACS ,what do you think

[gmx-users] force field for selinomethionine?

Dear gromacs users, I have to do simulations for a peptide which has the selinomethionine. But regular force fields from gromacs has no information for this residue. kindly give me information if is there any force field for selinometheoinine. Thanks in advance Surya Graduate student India. --

Re: [gmx-users] Problem in calculating static dielectric constant of Lysozymes

On 31/10/17 20:56, Suman Das wrote: Dear Gromacs Users, I am trying to calculate static dielectric constant of Lysozymes using gromacs version 4.6.7. I tried to follow the protocol used earlier by van Gunsteren (J. Phys. Chem. 1993, 97, 2009-2014). I used PME for the electrostatic interaction.