Re: [gmx-users] looping job: time not updating

On Mar 14, 2014 1:04 AM, gromacs query gromacsqu...@gmail.com wrote: Hi Jutsin Thanks, I was thinking that .cpt has all the information which I assumed would work like AMBER restart file to read time from .cpt (~ amber restart) file. It does, but the grompp workflow creates the opportunity

Re: [gmx-users] h_bonds

On Mar 14, 2014 4:27 AM, virk virkbl...@yahoo.com wrote: Dear Justin, Thanks for feedback...The percentage of glycine molecules that exist as monomers (i.e., with no hydrogen bonding to any other glycine molecule), dimers (i.e., pairs of glycine molecules hydrogen bonded to each other but

Re: [gmx-users] Dubious results with NPT

Hello, This time I tried sesiisotropic scaling with Berendsen Barostat. The compressibility was set to zero in Z-direction allowing scaling only in X and Y. The NPT simulation was run for 10ns. The result did not look good and the average pressure was ~36 bar (reference pressure is 1 bar).

[gmx-users] genion

Dear gromacs users In genion tool of gromacs, there are only Na and Cl ions. I want to add Zn2+ ions to my system. How to add these ions with special concentration? Any help will highly appreciated -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] multi threading on rocks cluster

On Fri, Mar 14, 2014 at 10:46 AM, michael.b mbx0...@yahoo.com wrote: dear all, I have a problem with multithreading on a cluster. Our (vanilla) rocks cluster has several nodes each with 8 cores. I used to be able to start a job with mdrun_d -nt 8 (NOT mdrun_mpi) and the directive -pe

Re: [gmx-users] Dubious results with NPT

The simplest explanation would be that you've appended to a previous 5ns trajectory, not run a new trajectory. Check the .log file and the length of time you expected this job to run (wall and simulation). Mark On Fri, Mar 14, 2014 at 9:02 AM, sujithkakkat . sujithk...@gmail.comwrote: Hello,

[gmx-users] asking for N and C termini for DNA and giving error

Hello, My protein is pr-DNA complex, it is identifying DNA terminus and searching for N and C in tdb file giving error. When I select -ter and specify none as termini , it still gives error saying There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a

Re: [gmx-users] g_tune_pme scalevdw option not working?

Dear João, could you check whether https://gerrit.gromacs.org/#/c/3267/ fixes your problems with g_tune_pme? Thanks, Carsten On 13 Mar 2014, at 18:27, João Rodrigues anar...@gmail.com wrote: Hi Carsten, Thanks for the reply and for the info on the rlist modification. I created the

Re: [gmx-users] g_tune_pme scalevdw option not working?

Hi Carsten, Thanks for the fix! Will run it today and get back to you with the results. Cheers, João 2014-03-14 12:32 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Dear João, could you check whether https://gerrit.gromacs.org/#/c/3267/ fixes your problems with g_tune_pme? Thanks,

Re: [gmx-users] Dubious results with NPT

Hello Mark, I guess you were asking whether I ran the simulation as a continuation to a previous 5ns run? But the results I got are from a continuous 10ns simulation. Sujith. On Fri, Mar 14, 2014 at 4:28 PM, Mark Abraham mark.j.abra...@gmail.comwrote: The simplest explanation would be

Re: [gmx-users] g_tune_pme scalevdw option not working?

Checked. Fixed. Thanks again! João 2014-03-14 14:03 GMT+01:00 João Rodrigues anar...@gmail.com: Hi Carsten, Thanks for the fix! Will run it today and get back to you with the results. Cheers, João 2014-03-14 12:32 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Dear João, could you

[gmx-users] Free energy calculation of a charged system

Hello, I need an advise on how it is better to approach the ThermoD integration of such system: +vely charged inorganic layer, filled with water and counterbalanced by -ve organics Do I integrate out organics both VdW and Coulomb, making the system have total +ve charge at lambda = 1 OR: Do I

Re: [gmx-users] Free energy calculation of a charged system

Hi Valentina - Honestly, I did not get the considerations with charges. TI probably scales interaction energies between selected groups, not charges. Science-wise, I would first decouple organic particle, then decouple chloride anions, and place a right sign between these two free energies. If

[gmx-users] Position restraints

I have a .top file looking like this: #include spc.itp #include ffgmx.itp #include lipid.itp #define POSRES_LIPID #include mylipid.itp #include dppc.itp [ system ] test system [ molecules ] ; Compound        #mols DX5                 200 DPPC        200 The #define POSRES_LIPID is used

[gmx-users] Rigid water model

Hi! I tried to reproduce results for rigid water with 895 molecules~1000 kg/m3 density, 10 ns NPT simulation (298 K 1 bar)with Parinello Rahman Barostat and Berendsen thermostat. Here is my result for SPC water Kappa (J/m3)5.689E-10 Cp 22.8054 Cp- Cv 5.94102 The density,