[gmx-users] NPT and NVT eqquilibruim - membrane simulation

The answer depends on what you are doing and where you got your starting structure. Please provide more information. Generally, if you are in doubt, then do NVT prior to NPT. Nevertheless, going straight to NPT is often ok. -- original message -- I'd like to know if it is necessary to run NVT

Re: [gmx-users] Interaction energy..

Hi justin, the out put of g_energy are like - 1 G96Angle 2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.

[gmx-users] NPT and NVT eqquilibruim - membrane simulation

Hi all, I'd like to know if it is necessary to run NVT and NPT equilibrium on a membrane-water system? Would only the NPT be sufficient? How can I understand it? Thanks in advance. Sincerely, Shima  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

[gmx-users] About pritein Lipid Bilayer Simulation

Dear Justin , Thank you for your Previous reply using Genbox I have  Successfully Solvated  Energy Minimized  "System_shrink.gro" file  It adds 84266 water molecules .  Then  Tutorial How to Check Existence of Water Molecules within HydroPhobic  core of Bilayer  it is  D

Re: [gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible

On 10/5/12 5:19 PM, Sonia Aguilera wrote: Thank you a lot, I only changed the couple-intramol setting (couple-intramol=yes) and now it´s running just fine. However I have a doubt about something. In the manual says the following when using couple-intramol=no "In this manner the decoupled stat

Re: [gmx-users] Re: Segmentation fault, mdrun_mpi

On 10/5/12 3:03 PM, Ladasky wrote: Bumping this once before the weekend, hoping to get some help. I am getting segmentation fault errors at 1 to 2 million cycles into my production MD runs, using GROMACS 4.5.4. If these errors are a consequence of a poorly-equilibrated system, I am no longer

Re: [gmx-users] residue-residue interaction energies

On 10/5/12 1:40 PM, federico vaglio wrote: Dear all, I would like to extract the interaction energies (LJ and electrostatic) between each residue pairs from my trajectory. The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm, LJ-SRemat.xpm, totalemat.xpm) but not a "data" file wi

[gmx-users] A question on REMD result analysis

Most often, people only analyze conformations drawn from the target temperature (e.g. room temperature). There are reasons to look at higher temperatures (e.g. to decompose entropy/enthalpy or if your system has biologically or chemically relevant temperature-dependence) but you can probably i

[gmx-users] Re: Error There is no domain decomposition for 6 nodes that is compatible

Thank you a lot, I only changed the couple-intramol setting (couple-intramol=yes) and now it´s running just fine. However I have a doubt about something. In the manual says the following when using couple-intramol=no "In this manner the decoupled state of the molecule corresponds to the proper v

Re: [gmx-users] Interaction energy..

On 10/5/12 1:26 PM, rama david wrote: Hi, I got the result by g_energy. Thank you for these . but when I used g_enemat with the edr file ( out put from mdrun -rerun ) g_enemat -f ener.edr -groups groups.dat i got following out put roup 0WARNING! could not find group (null):extra34-extra34 (

[gmx-users] Re: Segmentation fault, mdrun_mpi

Bumping this once before the weekend, hoping to get some help. I am getting segmentation fault errors at 1 to 2 million cycles into my production MD runs, using GROMACS 4.5.4. If these errors are a consequence of a poorly-equilibrated system, I am no longer getting the right kind of error message

[gmx-users] (no subject)

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[gmx-users] residue-residue interaction energies

Dear all, I would like to extract the interaction energies (LJ and electrostatic) between each residue pairs from my trajectory. The g_enemat tool generates only 3 xpm image files (Coul-SRemat.xpm, LJ-SRemat.xpm, totalemat.xpm) but not a "data" file with the residue-residue interaction energies I'm

Re: [gmx-users] Interaction energy..

Hi, I got the result by g_energy. Thank you for these . but when I used g_enemat with the edr file ( out put from mdrun -rerun ) g_enemat -f ener.edr -groups groups.dat i got following out put roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find

Re: [gmx-users] Error with "grompp"

On 10/5/12 1:00 PM, Elie M wrote: I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following: 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in ff

Re: [gmx-users] Interaction energy..

Hi justin, Ok now I get I have to modify mdp parameter .. Thank you, With best wishes and regards, Rama david On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul wrote: > > > On 10/5/12 11:46 AM, rama david wrote: > >> Thank you for your Help. >> >> I did the following tc-groups >> >> tcoupl=

RE: [gmx-users] Error with "grompp"

I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following: 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in fftoplsaa.nb and see to what symbol the

Re: [gmx-users] Interaction energy..

On 10/5/12 11:46 AM, rama david wrote: Thank you for your Help. I did the following tc-groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= extra34 Non-Protein energy; two coupling groups - more accurate tau_t= 0.10.1 0.1; time constant

Re: [gmx-users] Re: vacuum simulation problem with pdb file

On 10/5/12 11:15 AM, pauladelgado wrote: Thanks for your reply, Why could it happen? Can i do something to fix it? http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul, Ph.D. Research

Re: [gmx-users] Interaction energy..

Thank you for your Help. I did the following tc-groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= extra34 Non-Protein energy; two coupling groups - more accurate tau_t= 0.10.1 0.1; time constant, in ps ref_t= 310310 310

Re: [gmx-users] Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

On 2012-10-04 11:50, Emma Eriksson wrote: Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull par

[gmx-users] A question on REMD result analysis

Dear Gromacs users, I’m trying to run a REMD simulation on a protein. After a lot of reading, I am still unclear on the result analysis. Is it correct that, of many replicas, I should select the frames from only the replica with my desired temperature?(ex, room temp.) If not correct, how do I s

[gmx-users] Re: vacuum simulation problem with pdb file

Thanks for your reply, Why could it happen? Can i do something to fix it? Paula -- View this message in context: http://gromacs.5086.n6.nabble.com/vacuum-simulation-problem-with-pdb-file-tp5001688p5001693.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users

Re: [gmx-users] About Protein in Bilayer Simulation

On 10/5/12 10:39 AM, vidhya sankar wrote: Thank you Justin For Your Previous reply Finally Somehow I have Adjusted The Cut-Off and Grid Size and Inserted Protein in Lipid By Deleting some Lipid Molecules MY Question is 1) W

[gmx-users] About Protein in Bilayer Simulation

Thank you Justin For  Your Previous reply Finally Somehow I have  Adjusted  The Cut-Off  and  Grid Size and Inserted Protein in Lipid By Deleting some Lipid Molecules  MY Question is  1)  When I am Using inflategro  Perl  Script ,I n

Re: [gmx-users] vacuum simulation problem with pdb file

On 10/5/12 10:16 AM, Paula Andrea Delgado Pinzon wrote: Hi all, I am trying to do a vacuum simulation with distance restrain, first i did an EM without distance restrastraints, later i did 100 ps to stabilized the T at 300 K but i get this in the pdb file ATOM 1 N MET 1 na

Re: [gmx-users] Interaction energy..

On 10/5/12 10:16 AM, rama david wrote: Hi gromacs friends, I completed the simulation of receptor and ligand, I visualized the trajectory in the vmd I found most of the time C terminal (ARG) interact with receptor ( 320 ASP) . I want to find out these interaction energy between these two resi

[gmx-users] vacuum simulation problem with pdb file

Hi all, I am trying to do a vacuum simulation with distance restrain, first i did an EM without distance restrastraints, later i did 100 ps to stabilized the T at 300 K but i get this in the pdb file ATOM 1 N MET 1 nan nan nan 1.00 0.00 ATOM 2 H1 MET 1

Re: [gmx-users] cut-off g_hbond

O.K thanks Justin Lemkul wrote: > > > On 10/5/12 8:15 AM, Gavin Melaugh wrote: >> Is there any need to use the r2 option the ? >> > > That option is not relevant here. It is undocumented in the current > release, but the help description has been updated for the next release: > > http://redmine.g

Re: [gmx-users] cut-off g_hbond

On 10/5/12 8:15 AM, Gavin Melaugh wrote: Is there any need to use the r2 option the ? That option is not relevant here. It is undocumented in the current release, but the help description has been updated for the next release: http://redmine.gromacs.org/projects/gromacs/repository/revisi

Re: [gmx-users] cut-off g_hbond

Is there any need to use the r2 option the ? Justin Lemkul wrote: > > > On 10/5/12 7:39 AM, Gavin Melaugh wrote: >> Hi Justin >> >> Thanks, that's what I thought. Is there a need to define a >> hydrogen-acceptor distance as well. I read in a few articles that this >> was the case, usually 0.25nm ?

Re: [gmx-users] cut-off g_hbond

On 10/5/12 7:39 AM, Gavin Melaugh wrote: Hi Justin Thanks, that's what I thought. Is there a need to define a hydrogen-acceptor distance as well. I read in a few articles that this was the case, usually 0.25nm ? One can define hydrogen bonds in a number of ways, but a D-A distance of 0.35 n

Re: [gmx-users] Interaction energy calculation..

Hi justin, thank you for reply. With best wishes and regards Rama david. On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul wrote: > > > On 10/5/12 6:15 AM, rama david wrote: > >> Hi justin, >> I completed the simulation , >> Now I want to use the selected residues of protein and ligand. >> How to

Re: [gmx-users] cut-off g_hbond

Hi Justin Thanks, that's what I thought. Is there a need to define a hydrogen-acceptor distance as well. I read in a few articles that this was the case, usually 0.25nm ? Cheers Gavin Justin Lemkul wrote: > > > On 10/5/12 7:20 AM, Gavin Melaugh wrote: >> Hi all >> >> I am using g_hbond to calcu

Re: [gmx-users] help

On 10/5/12 7:20 AM, Marlon Hinner wrote: Please unsubscribe. Thank you. Per the instructions in the footer of every mail on the list: * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. -Justin -- ===

Re: [gmx-users] cut-off g_hbond

On 10/5/12 7:20 AM, Gavin Melaugh wrote: Hi all I am using g_hbond to calculate the number of hydrogen bonds in an alcohol system. I am using the following command: g_hbond -f traj.trr -nonitacc I am slightly confused about the cut off r. Using the above command, is the default cut-off r (0.

[gmx-users] cut-off g_hbond

Hi all I am using g_hbond to calculate the number of hydrogen bonds in an alcohol system. I am using the following command: g_hbond -f traj.trr -nonitacc I am slightly confused about the cut off r. Using the above command, is the default cut-off r (0.35nm) for the donor-acceptor distance or the

[gmx-users] help

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[gmx-users] Free energy calculation on a frozen fragment

Hi all, I'm interested in calculating the free-energy change when a frozen part of the system changes. The change, in general, implies a change in coordinates and in non-bonded parameters. As far as I know, there's no efficient way to calculate this currently in gromacs. The only way I see is

Re: [gmx-users] Interaction energy calculation..

On 10/5/12 6:15 AM, rama david wrote: Hi justin, I completed the simulation , Now I want to use the selected residues of protein and ligand. How to do it Would you explain me in detail?? Create a new .tpr file from an .mdp file with suitable energygrps. Use mdrun -rerun to recalculate ene

Re: [gmx-users] Interaction energy calculation..

Hi justin, I completed the simulation , Now I want to use the selected residues of protein and ligand. How to do it Would you explain me in detail?? With best wishes and regards, Rama david. On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul wrote: > > > On 10/5/12 5:49 AM, rama david wrote: > >>

Re: [gmx-users] Interaction energy calculation..

On 10/5/12 5:49 AM, rama david wrote: Hi Friends, I want to study the interaction energy between the selected residues of protein and ligand. ( Non-bonded energy should include : vanderwall and electrostatics) How to do it??? This is what the energygrps keyword in the .mdp file is for. B

Re: [gmx-users] Error There is no domain decomposition for 6 nodes that is compatible

On 10/5/12 5:35 AM, lloyd riggs wrote: you have to play with the ratio usually of domain decompositions Vs. Grid size, I had that error some time ago though, if you look at the generated .mdp from the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and play with it.

Re: [gmx-users] PME error for energy minimization of TMD in lipid bilayer

On 10/5/12 5:20 AM, Archana Sonawani wrote: Dear gromacs users, I am energy minimizing the TMD (286 residues) in lipid bilayer for inflategro step. I am getting the following error. Analysing residue names: There are: 287Protein residues There are: 127 Other residues Analysing Pr

Re: [gmx-users] The No. of the CO2 melecules in top file can not be updated correctly

On 10/5/12 5:18 AM, Bao Kai wrote: Hi, Justin, Thank you for your reply. It is a little weird and inconvienient that genbox does not update the No. of solute molecules. Is it designed in this way? Does it have any reason for that? The principal function of genbox is to solvate systems, us

Re: [gmx-users] Error There is no domain decomposition for 6 nodes that is compatible

you have to play with the ratio usually of domain decompositions Vs. Grid size, I had that error some time ago though, if you look at the generated .mdp from the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and play with it. It dosent like odd numbers or non-whole d

[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly

Hi, Justin, Thank you for your reply. It is a little weird and inconvienient that genbox does not update the No. of solute molecules. Is it designed in this way? Does it have any reason for that? For my case, the inear, 3-atom model of CO2 works pretty well. I got the model from a paper from Z

[gmx-users] regarding g_covar

Hello Everybody, I am using g_covar with -xpmc flag in-oder to generate matrix of atomic correlation coefficients. At present I am using g_covar script given by Ran, which I downloaded from gromacs user modified script pool. Since Ran's script is for gromacs 3.3.3 and it not accept .trp input fro