[gmx-users] NVT Equilibration

Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md  ; leap-frog integrator nsteps  = 5  ; 2 * 5 = 100 ps dt  = 0.002  ; 2 fs tcoupl  = V-rescale ; modified Berendsen thermostat The syst

Re: [gmx-users] making movie from trajectories

On 26/11/2011 1:55 AM, Saman Mandegar wrote: Dear All, I would like to make a movie from my trajectories using vmd. I need to make a movie which during the simulation the color of model is changing after some frames during the dynamics (showing the transition between two states), this is accom

Re: [gmx-users] QM/MM energies

Dear Jon, To the best of my knowledge the potential energy is the sum of all energies (E_QM + E_MM + E_QM/MM). The quantum energy (actually I do not see it in my output) for electrostatic embedding includes E_QM + E_QM/MM(el.stat.). I.e. E_QM/MM(VDW) you have to extract from the edr file. You

[gmx-users] translational diffusion of the water at the micelle surface

Hi everybody, I would like to compute the translational diffusion around the micelle surface. I know that I can select the water molecules at x distance of the micelle surface with g_select (right ?) but how to use this file generated by g_select to compute de diffusion, since the index and/or

[gmx-users] making movie from trajectories

Dear All, I would like to make a movie from my trajectories using vmd. I need to make a movie which during the simulation the color of model is changing after some frames during the dynamics (showing the transition between two states), this is accompanied by showing the change in time clock and

[gmx-users] q4md-forcefieldtools.org announcement

Dear All, I am pleased to announce the official release of the latest developments at http://q4md-forcefieldtools.org. q4md-forcefieldtools.org regroups an ensemble of tools, server, database and tutorials related to empirical force field developments. Theses developments are designed for

[gmx-users] Re: gmx-users Digest, Vol 91, Issue 184

Miło mi to słyszeć. W takim razie czekam na przesyłkę. Pozdrawiam, Sławomir Stachura Wiadomość napisana przez gmx-users-requ...@gromacs.org w dniu 2011-11-25, o godz. 12:00: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the

[gmx-users] QM/MM energies

Dear gmx users, I am performing some QM/MM optimizations using the ORCA interface in order to compare the energies of different structures of the same system. However, I have some questions related with the energy terms. In the output file the "potential" and "Quantum Ener." terms are printed out

Re: [gmx-users] multiple molecules simulations

Thank you Tsjerk, this is encouraging for me! Gloria Da: Tsjerk Wassenaar A: Gloria Saracino ; Discussion list for GROMACS users Inviato: Venerdì 25 Novembre 2011 10:10 Oggetto: Re: [gmx-users] multiple molecules simulations Hi Gloria, It think it's pre

Re: [gmx-users] Pressure stabilization during NPT phase

Oh, I see I forgot to state that X should be set to the trajectory name: X=/some/where/trajectory.xtc python -c 'X=open("'$X'").read(); print X[X.rfind(X[:8]):]' > last.xtc or just python -c 'X=open("/some/where/trajectory.xtc").read(); print X[X.rfind(X[:8]):]' > last.xtc Cheers, Tsjerk On F

Re: [gmx-users] multiple molecules simulations

Hi Gloria, It think it's pretty obvious that loose pieces will see one another across periodic boundaries diffusing around the place. Whether it's a good model of reality is something for you to verify. A priori, the approach seems fine. Cheers, Tsjerk On Fri, Nov 25, 2011 at 8:46 AM, Gloria Sa

Re: [gmx-users] Pressure stabilization during NPT phase

Hey, You don't actually need to copy the trajectory. trjconv and other tools are comfortable operating on an unfinished trajectory. They'll just bail out at the end. As an alternative, here's a python one-liner to extract the last frame (along with unfinished frames) from an XTC trajectory: pytho

[gmx-users] vol in mdrun output

"vol 0.63! imb F 25% pme/F 0.99 step 16389600..." What does vol 0.63! stand for ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't p

Re: [gmx-users] grompp error

Yes I find the in the mdp file I wrote "tc-grps=Ptotein Other". Sorry for this stupid error. Thank you. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 1

Re: [gmx-users] grompp error

I think the same with you sir. But I just cann't find where I make this typing error of "Ptotein". I checked my md.mdp and RI-10.top and dind't find such a typo. Could you suggest any possible locations of this typo? Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE

Re: [gmx-users] about relaxation protocol

Hi Tsjerk: I only found free energy calculation in the manual but there is nothing related to free energy pertubation stuff. Does anybody get related .mdp/scrips to do so ? I would like to relax my system very steadily. THX -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

[gmx-users] calculating the pmf in constrained force simulations

Hi I do constrained force simulations and i have the pullf.xvg and pullx.xvg files.. I want to know how to calculate the force for each simulation and i how to integrate the forces.. can some one help me. Ramya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

Re: [gmx-users] grompp error

The most reasonable thing is that there is a typo in your .mdp or in your .top files. Check where you've written "Ptotein" instead of Protein On 11/25/11 4:09 PM, yp sun wrote: Dear Sir' When I ran the grompp as following grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr a error information

Re: [gmx-users] grompp error

On 25/11/2011 7:09 PM, yp sun wrote: Dear Sir' When I ran the grompp as following grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr a error information appeared: Program grompp, VERSION 3.3.1 Source code file: readir.c, line: 789 Fatal error: Group Ptotein not found in indexfile Maybe you hav

[gmx-users] grompp error

Dear Sir'   When I ran the grompp as following   grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr   a error information appeared:     Program grompp, VERSION 3.3.1 Source code file: readir.c, line: 789 Fatal error: Group Ptotein not found in indexfile Maybe you have non-default goups in your

Re: [gmx-users] Pressure stabilization during NPT phase

On 25/11/2011 6:53 PM, James Starlight wrote: This way I've already used but is this possible to extract Gro and trp files from uncompleated runs and not stopping this simulation ? Copy the trajectory file. Then use trjconv on the copy however suits you. You don't need a new .tpr, you need eit