[gmx-users] The octahedron problem

Dear Gromacs Users, I have the problem with generating the octahedron box. I always get the rectangular box (using VMD) When I searched on the gmx maillist, I saw some people met same problem. Is problem is normal in gromacs? After run simulation, I can display the trajectory on VMD by using the

Re: [gmx-users] Problem control output for checkpoint file

to support XTC writing. You can always use trjconv to post-process out the groups or steps you want, etc. Mark On Tue, May 19, 2015 at 4:13 PM Justin Lemkul jalem...@vt.edu wrote: On 5/19/15 10:10 AM, Vy Phan wrote: Dear Justin Lemku, I am so thankful for your help Could you please

[gmx-users] Generate the water box

Dear Gromacs Users, Can I generate only water on the Gromacs? I need water box only. Thank you Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] .trr file

Hi, Put the command line nstout, nstout (Output control-chapter 5-Gromacs manual) on your mdp file. Phan Vy 2015-06-05 13:36 GMT+09:00 Swapnil Kate swapnilk...@rocketmail.com: hello, These are my files, in EM step it is generating .trr file and in NVT and NPT it coulden't. I am still

Re: [gmx-users] Center of mass motion removal

with an error. Also, if you think of fooling the program in this way, you may be assumed to know what you're doing (and why you wouldn't need to worry about flying ice cubes). Cheers, Tsjerk On Jun 3, 2015 8:23 AM, Vy Phan phanvy120...@gmail.com wrote: Dear Tsjerk and all, If I set up the comm

Re: [gmx-users] Tutorial site down

Dear Justin, I hope all thing will be on its road soon :) Tuong Vy 2015-06-02 23:12 GMT+09:00 Justin Lemkul jalem...@vt.edu: All, Yesterday we experienced a hardware failure on the server that hosts my GROMACS tutorials. We are aware of the issue and are going to be setting up a new

[gmx-users] Center of mass motion removal

Dear all, I wonder when I set the comm-mode =Linear , and nstcomm (frequency for COM motion removal) nststeps (maxinum number of steps), the MD simulation can be performed. I think the nstcomm nsteps mean COM motion is not removed (the MD simulation can be not performed) Could somebody explain

[gmx-users] epsilon-r

Dear Gromacs Users, I do not know how to set up the epsilon-r and epsilon-rf in simulation with spc model water. I set it as default value (epsilon-r =1 and epsilon-rf =0). Is it right? Thank you so much Tuong Vy -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Building topologies manually

Dear Gromacs Users, I want to simulate the protein s-glutathionylation. The problem is how to build the topologies for glutathione ([image: $\gamma$]-Glu-Cys-Gly). Could someone give me some suggestion and experiences? Thank in advance Tuong Vy -- Gromacs Users mailing list * Please search

Re: [gmx-users] Making disulfide bonds between protein and glutathion (GSH)

Many thanks Justin :) Tuong Vy 2015-05-28 21:01 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/27/15 10:23 PM, Vy Phan wrote: Dear Gromas User, I want to making disulfide bonds between protein and glutathion (GSH). The topology for GSH I got from Produg serve. Don't do

[gmx-users] Making disulfide bonds between protein and glutathion (GSH)

Dear Gromas User, I want to making disulfide bonds between protein and glutathion (GSH). The topology for GSH I got from Produg serve. Could you please show me how I can make the disulfide bons between protein and GSH? Thank you so much Tuong Vy -- Gromacs Users mailing list * Please search

[gmx-users] Topology for Ligand from Prodrg server and force field 54a7 for protein

Dear Gromacs Users I use the force field 54a7 for protein. Can I simulate the protein-ligand complex with topology of ligand get from PRODRG server. Thanh in advance Tuong Vy -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Building topologies manually

Dear Justin, I am so thankful for your reply. I still do not know how I can build the topology for the [image: $\gamma$] -Glu. I want to use gromos force field 54a7. Could you give some more guideline? Tuong Vy 2015-05-28 5:27 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/27/15 9:41 AM, Vy

[gmx-users] LINSC WARNING

Dear Gromacs Users, When I run npt equilibrium, I set the step size is 4fs. I go many LINCS WARNING bonds that rotate more than 30 degrees When I reduce the step size to 2fs. All thing is fine. Could someone here explain to me? Finally, I want to use step size is 4fs. Any suggestions for me?

[gmx-users] restraint one part of protein

Dear All, I got the pdb file from protein Data Bank with some missing loop. I use swissmodel to add the missing loop. In energy minimization step, I want to relax these loops and restraint the crystal structure. How can I generate the restraint file? Could someone help for this jobs? Tuong Vy --

[gmx-users] High density

Dear all, My system includes protein and spc water. After running 1000ps NPT equilibrium I got the density is 1010+/-1.25. I hope I can get the density is 1000kg/m3. I run for a long NPT step, I still get around 1010. Is this value is fine ? Do I need to run more? Tuong Vy -- Gromacs Users

[gmx-users] Run NVT equilibrium

Dear all, I wonder why , on some tutorial, running NVT equilibrium we need only the em.gro (the final coordinate of energy minimization step) . why do we not need em.edr ? Thank a lot Tuong VY -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Run NVT equilibrium

Thank a lot for your clearly explanation. Tuong Vy 2015-05-24 0:28 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/23/15 10:40 AM, Vy Phan wrote: Dear all, I wonder why , on some tutorial, running NVT equilibrium we need only the em.gro (the final coordinate of energy minimization step

Re: [gmx-users] Generate the water box

wrote: genbox without adding a protein. More specifically (and for 5.0): gmx solvate -cs water.gro -box (whatever size is needed) -Justin On Wed, May 20, 2015 at 9:56 AM, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, Can I generate only water on the Gromacs? I need

Re: [gmx-users] LINSC WARNING

Thank a lot for your suggestion. Tuong VY 2015-05-22 20:21 GMT+09:00 Mark Abraham mark.j.abra...@gmail.com: Hi, Start by learning what makes a time step stable, e.g. manual 6.8 Mark On Fri, May 22, 2015 at 10:51 AM Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, When I run

Re: [gmx-users] restraint one part of protein

thank you so much Justin Tuong Vy 2015-05-26 20:40 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/26/15 6:58 AM, Vy Phan wrote: Dear All, I got the pdb file from protein Data Bank with some missing loop. I use swissmodel to add the missing loop. In energy minimization step, I want

Re: [gmx-users] infinite force at the membrane lipid

I hope you can give more recommendations. Removing lipids actually is not an appropriate solution. Thank you so much Tuong Vy 2015-08-16 1:47 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 8/15/15 12:41 PM, Vy Phan wrote: Dear All gromacs Users, I want to run the membrane protein

Re: [gmx-users] infinite force at the membrane lipid

+0900 From: Vy Phan phanvy120...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] infinite force at the membrane lipid Message-ID: CAC+3Te00hidSrXE49g5mfqvCsBSaE5wTJ-NtFubaXvvz= u6...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Dear Dr Justin and Gromacs User

[gmx-users] Charmm 36 parameter file for gromacs

Dear Gromacs users, On the .itp file on the charmm36 force field, I see the DOPC and other lipid which have the [atom][bond] and [ impropers] parameter. I wonder where is the parameter for [dihedrals]. please help me! Thank in advance Tuong Vy -- Gromacs Users mailing list * Please search the

[gmx-users] Topology for DOPC lipid Charmm36 ff

Dear Gromacs users, I want to run tranmembrane protein with Gromacs code and using Charmm 36 ff. I tried to search the the topology for DOPC, I couldn't find. Could someone here help me? Thank in advance Phan Vy -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Topology for DOPC lipid Charmm36 ff

at 05:51, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs users, I want to run tranmembrane protein with Gromacs code and using Charmm 36 ff. I tried to search the the topology for DOPC, I couldn't find. Could someone here help me? Thank in advance Phan Vy -- Gromacs Users

[gmx-users] Can not run energy minimization for the protein-lipid system.

Dear Gromacs Users I run membrane protein with DOPC lipip. Without protein, the lipid-ions-water system can run energy minimization. But when I insert protein in the center of that system (I removed the overlapping molecules), but this system can not run. I always got this message. Actually, I do

Re: [gmx-users] Charmm 36 parameter file for gromacs

...@vt.edu: On 8/11/15 10:01 AM, Vy Phan wrote: Dear Gromacs users, On the .itp file on the charmm36 force field, I see the DOPC and other lipid which have the [atom][bond] and [ impropers] parameter. I wonder where is the parameter for [dihedrals]. Angles and dihedrals are automatically

Re: [gmx-users] Charmm 36 parameter file for gromacs

please. Dear Dr. Justin Thank you so much for your suggestion. I will try with CHARMM-GUI. Best regards, Tuong Vy 2015-08-12 21:19 GMT+09:00 Vy Phan phanvy120...@gmail.com: Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which

Re: [gmx-users] Charmm 36 parameter file for gromacs

Dear Dr. Justin I got your means and it is very helpful for me. Thank you so much :) Sincerely, Tuong Vy 2015-08-12 21:23 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 8/12/15 8:20 AM, Vy Phan wrote: Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download

[gmx-users] LINCS WARNING

Dear all gromacs Users! I want to run a simulation with the system protein-ligand (I have several ligands). With EM, nvt, npt step I put position restraint for the ligands and all thing was fine. After that, I run production simulation without position restraint of ligands. I saw the ligand move

Re: [gmx-users] LINCS WARNING

Dear Justin, I am so thankful for you kindly reply. Now, I can solve this problem. Tuong Vy On Tue, Oct 6, 2015 at 11:49 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/6/15 3:26 AM, Vy Phan wrote: > >> Dear all gromacs Users! >> I want to run a simulation

[gmx-users] generate angle restraint and dihedral angle restraint file

Dear Gromacs Users, Are there avaluable command line to generate the angle restraint and dihedral file automatically? Thank you so much Phan Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] generate angle restraint and dihedral angle restraint file

Thank you Justin ! Phan Vy On Tue, Sep 8, 2015 at 8:29 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/8/15 2:24 AM, Vy Phan wrote: > >> Dear Gromacs Users, >> >> Are there avaluable command line to generate the angle restraint and >> dihedral fil