[gmx-users] Problem to create topology using Amber force fields for single zitterionic amino acids.

Dear all, I wanna simulate a system made up of non covalent bonded glutamine residues in water using different force fields, one of them belongs to amber family (amber99sb-aldn). Problem using amber force field is that I am not able to generate topology for zwitterionic single glutamine residues.

Re: [gmx-users] gmx density scripting?

On 3/10/17 12:08 PM, Dayhoff, Guy wrote: Is there a simple way to script the gmx density tool as to circumvent the need to manually select the groups from within the program? i.e. is there a way to specify the groups during the command call such as: gmx density -f traj.xtc -s input.tpr -ng 2

[gmx-users] gmx density scripting?

Is there a simple way to script the gmx density tool as to circumvent the need to manually select the groups from within the program? i.e. is there a way to specify the groups during the command call such as: gmx density -f traj.xtc -s input.tpr -ng 2 -grps 5,8 where -grps lets me tell it what

Re: [gmx-users] Gromacs with Plumed

PS: Unfortunately cmake -D GMX_VERSION_SUFFIX="FOO" won't work so the gmxVersionInfo.cmake file needs to be manually edited/ -- Szilárd On Fri, Mar 10, 2017 at 5:59 PM, Szilárd Páll wrote: > Hi, > > The discussion will continue on gmx-developers, those interested in >

Re: [gmx-users] Question regarding calculation of thickness using GridMAT-MD

On 3/10/17 10:15 AM, ali.khourshae...@student.sharif.edu wrote: Dear Gromacs users, I've used Gridmat-MD to obtain the bilayer thickness and its output is as follow: 4.029 4.029 4.0735 3.928 3.9245 3.914 3.8955 4.1755 4.349 4.349 4.426 4.236 4.236 4.1215 4.007 4.007 4.037 4.199 4.029 4.029

Re: [gmx-users] I want to drag two atoms together with GROMCS SMD options.

On 3/10/17 2:56 AM, Vytautas Rakeviius wrote: Thanks, and now after some time I get:"Pull reference distance for coordinate 3 () needs to be non-negative"How to solve this error? Please provide the text of the relevant pull options that you're using. -Justin --

[gmx-users] Question regarding calculation of thickness using GridMAT-MD

Dear Gromacs users, I've used Gridmat-MD to obtain the bilayer thickness and its output is as follow: 4.029 4.029 4.0735 3.928 3.9245 3.914 3.8955 4.1755 4.349 4.349 4.426 4.236 4.236 4.1215 4.007 4.007 4.037 4.199 4.029 4.029 4.029 4.074 4.074 3.928 3.9175 3.914 3.914 4.1315 4.349 4.349

Re: [gmx-users] g_hbond problems

On 3/10/17 4:51 AM, andrea.cor...@unina.it wrote: I am trying to analyze the hydrogen bonds of my simulations by g_hbond. I am using an index file where I created two groups: one with acceptor atoms (carboxylic oxygen atoms in my structure) and another group with the water molecules. I got

[gmx-users] mwa error in g_anaeig

Hello all I want to calculate quasi harmonic entropy. For that, I am using the commands *g_covar -f file.xtc -s file.tpr -n index.ndx -ref -mwa * group C-alpha followed by *g_anaeig -v eigenvec.trr -entropy -temp 300* When I execute the g_anaeig command, I get an error Fatal error:

Re: [gmx-users] g_energy for comparing total energies of 2 similar systems

AFAIK the total energy is usually meaningless. If you want to compare the relative stability of a bound ion pair versus an unbound one I think you're better off doing e.g. umbrella sampling. Peter On 10-03-17 04:48, #SUKRITI GUPTA# wrote: > Dear all, > > > I have two systems: 1. metal ion in

Re: [gmx-users] Order parameter for double bonded lipids

Yes, on Lipidbook. The force field is termed GROMOS-CKP. The parameters aren't perfect but if you are wanting to go with a GROMOS united-atom force field, these are AFAIK the best PG ones available. Cheers Tom From:

Re: [gmx-users] need help !

Hi Thanks you for your help .The analyses of my MD work perfectly. - Mail original - De: "Mark Abraham" À: gmx-us...@gromacs.org Envoyé: Jeudi 9 Mars 2017 17:07:07 Objet: Re: [gmx-users] need help ! Hi, See also

[gmx-users] g_hbond problems

I am trying to analyze the hydrogen bonds of my simulations by g_hbond. I am using an index file where I created two groups: one with acceptor atoms (carboxylic oxygen atoms in my structure) and another group with the water molecules. I got a segmentation fault with the message: Select