Re: [gmx-users] out from the simulation box

huan wrote: i am doing simulation on wax ester, i am wonder why my esters sometimes are out from my simulation box at the end of the simulation? my box is cubic and 5nm x 5nm x 5nm in size. http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Mark __

[gmx-users] out from the simulation box

i am doing simulation on wax ester, i am wonder why my esters sometimes are out from my simulation box at the end of the simulation? my box is cubic and 5nm x 5nm x 5nm in size. thanks. scot. Get easy, o

Re: [gmx-users] G_sas reside area

tangxuan wrote: Hi,all Is there a fast way to compute the resides area at each time in the simulation process? I can get the resides area at some specific time, a slow way.For exmple, when I get the average reside area between 0 ps and 100ps and average reside area between 0 ps and 101 ps, i ca

[gmx-users] How to delete bad water molecules

/>>While minimizing,// be sure to include / //>>/ define=-DFLEXIBLE />> //>/ in your .mdp file / Just out of curiosity, why do you think minimization should be done with flexible water? I've gone the opposite direction and only minimize with steepest descents since that's the only minimizatio

Re: [gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1

submitting a bugzilla entry could be helpful in examining this case. On 11/17/2007 4:45 AM, Amadeu wrote: My student and I have been trying the latest Gromacs version (3.3.2) for the simulation of a CNT. We noticed that the bonded energies calculated with 3.3.2 are quite different compared to

Re: [gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1

Amadeu wrote: My student and I have been trying the latest Gromacs version (3.3.2) for the simulation of a CNT. We noticed that the bonded energies calculated with 3.3.2 are quite different compared to those from 3.3.1 (see resulting output below). Has anyone observed similar results? Was an

[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1

My student and I have been trying the latest Gromacs version (3.3.2) for the simulation of a CNT. We noticed that the bonded energies calculated with 3.3.2 are quite different compared to those from 3.3.1 (see resulting output below). Has anyone observed similar results? Was anything changed in 3.3

Re: [gmx-users] pressure coupling for bilayers

semiisotropic is more indicated for bilayers. pragya chohan <[EMAIL PROTECTED]> wrote: hi i want to rum a NPT ensemble on my bilayer+protein system. What is the best pcoupletype to use. I have seen some posts on gmx user group advising anisotriopic type with tau_p 5.0 ps cpmpressibility:

Re: [gmx-users] How to delete bad water molecules

Chris, > I don't know the answer to the exact question that you have posed, but > I instead suggest that getting rid of that water molecule is not a > good idea. You should rather minimize your system. While minimizing, > be sure to include > > define=-DFLEXIBLE > > in your .mdp file Just out of

[gmx-users] G_sas reside area

Hi,all Is there a fast way to compute the resides area at each time in the simulation process? I can get the resides area at some specific time, a slow way.For exmple, when I get the average reside area between 0 ps and 100ps and average reside area between 0 ps and 101 ps, i can get the reside a

RE: [gmx-users] position restrain

Thanks for your help. My simulation ran with your idea. > Date: Thu, 15 Nov 2007 13:34:40 -0500 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] position restrain > > If you read the documentation for genpr, it tells you th

[gmx-users] pressure coupling for bilayers

hi i want to rum a NPT ensemble on my bilayer+protein system. What is the best pcoupletype to use. I have seen some posts on gmx user group advising anisotriopic type with tau_p 5.0 ps cpmpressibility: 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 Another suggestion is welcome. Thanks in advance Pragya _

Re: [gmx-users] floating point exception for grompp -e ener.edr on some clusters

[EMAIL PROTECTED] wrote: Hello, I continue to have difficulties with my newest gromacs compilation (3.3.1). The errors that I report here are entirely absent from other clusters on which I have compiled gromacs. The error now is in grompp and looks like this: Opened sys1800_md689.edr as sing