Re: [gmx-users] Re: Use pull code to restrain the COM

On 8/9/13 12:48 PM, Bin Liu wrote: Hi Justin, Thank you for your quick reply. In Setting A, grompp reports Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 14623185-0.000 -0.000 -3.268

Re: [gmx-users] segmentation fault on g_protonate

On 8/9/13 2:35 PM, Pedro Lacerda wrote: Hi, My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb entry which I suppose being right. When running `g_protonate -s conf.pdb -o prot.pdb` to add the hydrogens happens an segmentation fault. The traceback for 4.6.4-dev-20130808-a

[gmx-users] segmentation fault on g_protonate

Hi, My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb entry which I suppose being right. When running `g_protonate -s conf.pdb -o prot.pdb` to add the hydrogens happens an segmentation fault. The traceback for 4.6.4-dev-20130808-afc6131 follows. I could add them by any othe

[gmx-users] Re: Use pull code to restrain the COM

Hi Justin, Thank you for your quick reply. In Setting A, grompp reports Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 14623185-0.000 -0.000 -3.268 6.668 6.693 6.492 The values of referen

[gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1

Hi, I just did the simulation with the last version of Gromacs (4.6.3) and it seems that the problem has disappeared!! Regards, Guillaume -- View this message in context: http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317p5010425.html Sent from

Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

Mark, Since I was working with 4.6.2, I built 4.6.3 to see if this was the result of a bug in 4.6.2. It isn't I get the same error with 4.6.3, but that is the version I'll be working with from now on, since it's the latest. Since the problem occurs with both versions, might as well try to fix

Re: Aw: [gmx-users] Umbrella sampling - position restraints

Thanks Justin, Stephan. I am running both and will post my observations soon. -- View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-sampling-position-restraints-tp5010405p5010422.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mail

Re: [gmx-users] GPU + surface

Hello. ¿Have you removed periodicity?. Because you may only be seeing traversal of water molecules among copies of the periodic system. Lucio Montero Ph. D. student Instituto de Biotecnologia, UNAM Mexico El 08/08/13 07:39, Ondrej Kroutil escribió: Dear GMX users. I have done simulation of

Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k

On 8/9/13 10:33 AM, Golshan Hejazi wrote: Hello, Thanks for the reply. I made another even more simple test. I just would like to understand what is going on inside the energy calculation. I have an ALA system. This is the topology file for the bond: [ bonds ] ; aiaj funct r k 1

Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k

Hello, Thanks for the reply. I made another even more simple test. I just would like to understand what is going on inside the energy calculation. I have an ALA system. This is the topology file for the bond: [ bonds ] ;  ai    aj funct  r  k     1     2     1  1.0100e-01  3.6317e+05     3    

Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate

On 2013-08-09 14:29, 朱文鹏 wrote: > Hello David, > > Thank you again for your reply. It is very interesting idea. > > Do you mean I can using a grand canonical ensemble to control the > surface tension of lipid bilayer by varying its number during my > simulations? Is there an existing method in

Re: [gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).

never done that calculation myself, so it's hard to say if these differences in the setup may account for such a free energy difference, but I remember one lecture by Phillipe Hünenberger a few years ago when he presented a large compilation of hydration free energies for sodium and the figures cha

Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate

Hello David, Thank you again for your reply. It is very interesting idea. Do you mean I can using a grand canonical ensemble to control the surface tension of lipid bilayer by varying its number during my simulations? Is there an existing method in Gromacs to implement so? Or I need to modify the

[gmx-users] gromacs-4.5.5 CPMD QM/MM

Dear All, I am planning to perform a QM/MM calculation of my protein system. Can anybody suggest me whether gromacs-4.5.5 can be patched with any latest version of CPMD? If not, then please suggest me some combination of the gromacs-cpmd versions. I came across this tutorial, but there, both groma

Re: [gmx-users] g_wham -sym

On 8/9/13 5:48 AM, Shima Arasteh wrote: Hi, I use the g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Use -zprof0. -Justin -- ===

[gmx-users] g_wham -sym

Hi, I use the  g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Thanks for your suggestions in advance.   Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs

[gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).

Thank you for posting. I also noticed they were using a spherical boundary model; you think using PBC would justify a 50 kJ/mol difference ? As for PME, we wanted to use the classical Ewald summation method, but it turns out that Gromacs hasn't implemented it, yet, for free energy of solvation calc