[gmx-users] Potential energy problem

Hi Gromacs users, I am doing the protein lipid system packing step and thus shrinking and minimizing the system alternately but after first minimization rest of all minimization steps show E pot=nan and no minimization step occurs in the em.log file. How to get rid of this problem? Please help.

Re: [gmx-users] Potential energy problem

On 14/09/2011 5:29 PM, madhumita das wrote: Hi Gromacs users, I am doing the protein lipid system packing step and thus shrinking and minimizing the system alternately but after first minimization rest of all minimization steps show E pot=nan and no minimization step occurs in the em.log file

[gmx-users] simulation with amber10 and gromacs 4.5.1

Hello Users, Previous I have done simulation of small protein using Amber10 with ff99sb force field. I did the same calculation using the gromacs 4.5.1 with amber ff99sb force field. I found a loop segment takes much more fluctuation with gromacs simulation and which was not observed with the

Re: [gmx-users] simulation with amber10 and gromacs 4.5.1

vijayaraj ramadoss wrote: Hello Users, Previous I have done simulation of small protein using Amber10 with ff99sb force field. I did the same calculation using the gromacs 4.5.1 with amber ff99sb force field. I found a loop segment takes much more fluctuation with gromacs simulation and whi

[gmx-users] Re: Gromacs_trouble

Please keep this discussion on the gmx-users list. I have only limited experience with MARTINI, but there are others on the list more experienced than I. See comments below. Du Jiangfeng (BIOCH) wrote: Dear Justin, Thank you very much again of your help. So far, I appended some sentences

Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

Hi, On 9/13/11 4:27 PM, Mark Abraham wrote: On 14/09/2011 12:20 AM, Marcin Zielinski wrote: Ok, Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors during the compilation. Firstly, including config.h inside the fortran .F kernel files for power6 is causing problems with their p

[gmx-users] equilibration: run time or number of steps?

Hello, For the equilibration one usually looks at the total energy or the observable of interest to be independent of time. I wanted to figure out when we are referring to equilibration which of the run time or n_steps parameters are important. One could run 1,000,000 steps with dt of 0.001 ps or

Re: [gmx-users] equilibration: run time or number of steps?

Juliette N. wrote: Hello, For the equilibration one usually looks at the total energy or the observable of interest to be independent of time. I wanted to figure out when we are referring to equilibration which of the run time or n_steps parameters are important. One could run 1,000,000 ste

Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

Hi, I have not followed the entire discussion so I might be completely wrong, I might be fill in some gaps. > Firstly, including config.h inside the fortran .F kernel files for power6 is > causing problems with > their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide a > modified x

Re: [gmx-users] equilibration: run time or number of steps?

On 15/09/2011 5:13 AM, Juliette N. wrote: Hello, For the equilibration one usually looks at the total energy or the observable of interest to be independent of time. I wanted to figure out when we are referring to equilibration which of the run time or n_steps parameters are important. One co

[gmx-users] Fwd: Gromacs_trouble

Hi, Please keep discussions on the mailing list. I have no experience of Martini, and don't have the ability to give my time for individual help. I would advise you to simplify your system as much as you can. Get a stable simulation of a single glutamate residue working, then change to a sing

[gmx-users] Re: strangeness in gro file

> > Hi Mark, I did a grompp without the temperature coupling and generated a .tpr file. From that I generated a .gro file using editconf. What it looks like now is it starts numbering from 1 -29, which is where the first monomer ends, again 1-29 for the second monomer and then its continuous

Re: [gmx-users] Re: strangeness in gro file

On 15/09/2011 11:23 AM, Sweta Iyer wrote: Hi Mark, I did a grompp without the temperature coupling and generated a .tpr file. From that I generated a .gro file using editconf. What it looks like now is it starts numbering from 1 -29, which is where the first monomer ends, again 1-29 for th

Re: [gmx-users] Re: strangeness in gro file

Mark Abraham wrote: On 15/09/2011 11:23 AM, Sweta Iyer wrote: Hi Mark, I did a grompp without the temperature coupling and generated a .tpr file. From that I generated a .gro file using editconf. What it looks like now is it starts numbering from 1 -29, which is where the first monome

Re: [gmx-users] how to handle different atom names between pdb and rtp files.

You can either use -ighn option in pdb2gmx or mannualy rename the atom names in the pdb file. Cheers, Jianguo From: KONG Xian To: gmx-users@gromacs.org Sent: Tuesday, 13 September 2011 15:36:41 Subject: [gmx-users] how to handle different atom names between

[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

Hi Alan, For example, in the Glycam_06g.dat file, you can find: OH-CG-CG-OS 1 -1.10 0.0-1 So this dihedral parameter has a force constant of -1.10, and this is what I mean by "GLYCAM force field assigns negative force constants to some dihedrals". I did

Re: [gmx-users] g_rms matrix between wt and mutant

Thanks Mark and Justin for your input. it works. For progeny, here's how: 1. In case of multiple, separate chains of protein, generate a *new* tpr X that does not include chain information. 2. From X generate a new tpr file Y, consisting now only of the group under scrutiny (for example, backbone.