[gmx-users] difference in Coulomb SR and Coulomb 14?

Dear experts, Can you please make me understand the actual difference between Coulomb SR and Coulomb 14? -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Strange problem.complex out of Box after EM

comes out of box from one side. can any body help me in fixing this problem so that i could proceed towards equilibrium steps.. Many thanks with anticipation Regards Saba -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan

[gmx-users] Re: gmx-users Digest, Vol 91, Issue 119

- > Regards, > Bipin Singh > > > -- > > Message: 2 > Date: Thu, 17 Nov 2011 06:51:43 -0500 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Strange problem.complex out of Box after EM > To: Discussion list for GROMACS use

[gmx-users] Protein Complex simulation

Dear Justin, I need to ask you that when we simulate 2 proteins and if the md.trr show both protein quite far then what can be inferred from this when the complex was simulated for 1ns. thanks with anticipation Regards -- Saba Ferdous Research Scholar (M. Phil) National Center for

[gmx-users] Increasing time for simulation

complex simulation, how much time would be enough to study the system in a good way as you told that 1ns is very short to study such type of system. many thanks -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- gmx-users

[gmx-users] restoration of crashed simulation

for the restoration? As this simulation was running since 6 days and I cant afford to restart it from the beginning:( Kindly tell me the full command to get it start from where it was stopped. Many thanks Regards -- Saba Ferdous Research Scholar (M. Phil) National Center for

[gmx-users] frames in 2 trajectory files

n one trajectory file while rest are in other which was created after resume. for analysis purpose I want all frames in one trajectory file. Can you tell me the way of doing so? waiting anxiously for help from your side. Thanks with anticipation Best Regards -- Saba Ferdous Research Scholar (M.

[gmx-users] Analysis of Protein Complex

simulations. Can you devise me a way to perform such kind of analysis. Further more I am interested to know the binding energies as well. What sort of other analysis can be done on this complex. -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University

[gmx-users] I want only coordinates in md.xtc/md.pdb

help me to get out of the broblem. I only want that my protein get display in vmd rather than the water box. the size of md-noPBC.xtc is 612 Mb md-noPBC.pdb is 13.2 GB analysis is getting very slow and system is hanging. kindly help me out to fix this problem. Regards Thanks -- Saba Ferdous

[gmx-users] Coulomb Energies

-- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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

[gmx-users] Coulomb Energy

-- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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

[gmx-users] Segmentation fault

dumped) saba@linuxserver:~/complex/MD> I used the command : ulimit -s unlimited ulimit -c unlimited but no vain, the problem still persists, Tell me how to fix it? I urgently need to study secondary structure during simulations Thanks... -- Saba Ferd