[gmx-users] HSE in Charmm-gui membrane builder

Dear gmx users, I am sorry for asking about charmm-gui . I would like to use HSE protonation state of HIS, and I am using Charmm-gui membrane builder. But, Charmm-gui only produces HSD protonation state in my initial system. How can I use HSE state? Best regards, Mijee -- Gromacs Users mailing l

Re: [gmx-users] Question about the No chi1 & chi2 angle problem with gmx Chi

On 8/19/17 1:21 PM, Xingcheng Lin wrote: Hi, I am using Gromacs function gmx chi to calculate the X1 and X2 angle based on my pdbs. However, it prompts this warnning: WARNING: not all dihedrals found in topology (only 317 out of 496)! No chi1 & chi2 angle for VAL7 No chi1 & chi2 angle for ALA

Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

On 8/19/17 8:23 AM, Alex Mathew wrote: Dear all, In order to obtain the PMF diagram of a water molecule through membrane protein channel, I set up a simulation system and try to run with pull_coord1_geometry= direction-periodic. To correct te error following changes are made in the mdp fil

Re: [gmx-users] umbrella sample Question

On 8/18/17 10:28 PM, yujie liu wrote: Thanks Justin, What do you means? I have carried out gmx distance to calculate the COM distance between two groups one by one through the previous confxxx.gro by myself, however I never met some fail or warnings. Finally, it seems that I can calculate

[gmx-users] Question about the No chi1 & chi2 angle problem with gmx Chi

Hi, I am using Gromacs function gmx chi to calculate the X1 and X2 angle based on my pdbs. However, it prompts this warnning: WARNING: not all dihedrals found in topology (only 317 out of 496)! No chi1 & chi2 angle for VAL7 No chi1 & chi2 angle for ALA13 ... However, the output seems to be compl

Re: [gmx-users] Use of providing -ix pullx.xvg in WHAM

Thanks Justin. Yogesh > On 18-Aug-2017, at 10:28 PM, Justin Lemkul wrote: > > > >> On 8/17/17 9:38 AM, jay patil wrote: >> Hello Experts, >> What property we can calculate by providing -ix pullx.xvg through gmx WHAM >> command. Like -if pullf.xvg can give PMF. > > You get a PMF. There are

Re: [gmx-users] problem in extending a simulation run

Thanks Mark > I want extend a 100ns run to 150 ns. For this I use following commands: I have these files from previous run before running following commands: ener.edr, md.log, traj.trr, traj_comp.xtc, state.cpt, state_prev.cpt > > gmx convert-tpr -s md_100ns.tpr -extend 5 -o md_150ns.tpr > >

[gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

Dear all, In order to obtain the PMF diagram of a water molecule through membrane protein channel, I set up a simulation system and try to run with pull_coord1_geometry= direction-periodic. To correct te error following changes are made in the mdp file {error (Can not have dynamic box while us

Re: [gmx-users] umbrella sample Question

Hi, This happens to me also for a long time and could not find any solution. There are no error messages coming when we execute the gmx distance. I ran the script multiple time to get a full set of distance data and execute the command separately for the missing one. -- Gromacs Users mailing list

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

yes, that is the problem, at the beginning everything seem to be ok, but letting the simulation run for some tens of ns (to have enough statistic), I have the LINCS warnings, so I will try to build manually the topology using the GROMOS ff building blocks, us you suggested, thank you again

[gmx-users] Simulated annealing

Dear gromacs users, I am extremely sorry for my previous incomplete mail. By mistaken I have pressed some short cut key. I have one peptide which has 25 residues. I have done simulation for 100ns. When I presented my analysis in lab, I was suggested to do investigation of my simulation by simul

[gmx-users] setting up simulated annealing

Dear gromacs users, I have one peptide which has 25 residues. I have done simulation for 100ns. When I presented my analysis in lab, I was suggested to do investigation of my simulation by simulated annealing. Then I have gone through the simulated annealing notes which I found on gromacs website