Re: [gmx-users] Potential Energy = -nan

shikha agarwal wrote: hi i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM Steepest Descents converged to Fmax 10 in 18 steps Potential Energy = -nan Maximum force = 4.7791553e+02 on atom 5440 Norm of force = -nan ;

Re: [gmx-users] Potential Energy = -nan

shikha agarwal wrote: hi I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . What is the hardware type? PowerPC, Intel 32- or 64-bit, etc? when i skiped scaling by factor 0.95 then , after EM step I m getting same potential energy nan result. Do other simple systems work?

Re: [gmx-users] Potential Energy = -nan

shikha agarwal wrote: hi, I m tried nstxout=1 in my .mdp file. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! The purpose of nstxout=1 is not to give you a different result. It might aid you in watching

Re: [gmx-users] Potential Energy = -nan

shikha agarwal wrote: hi, I tried on other system , 4GB ram , core i3 ,64bit processor ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent

Re: [gmx-users] potential energy NaN and strange dependence on cut-offs

Jennifer Williams wrote: Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent silica.) I keep this tube frozen. I start with an energy minimisation-however this runs to completion almost

Re: [gmx-users] potential energy NaN and strange dependence on cut-offs

Manik Mayur wrote: 2009/9/8 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Jennifer Williams wrote: Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is

Re: [gmx-users] potential energy NaN and strange dependence on cut-offs

2009/9/8 Mark Abraham mark.abra...@anu.edu.au Jennifer Williams wrote: Hi users, I am running a very simple simulation of methane inside a pore (v.much like a carbon nanotube but in my case the tube is supposed to represent silica.) I keep this tube frozen. I start with an energy

Re: [gmx-users] potential energy =nan

Am Mittwoch, 20. Juni 2007 schrieb Sheyore Omovie: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few

Re: [gmx-users] potential energy =nan

Sheyore Omovie wrote: I am doing an Energy Minimisation run for two polypeptides in a box. I get the range checking error, variable ci= and the simulation crashes. After changing ns_type to simple, the simulation is running, but very slowly and the first few steps return Epot=nan. What

Re: [gmx-users] potential energy =nan

. Rgds John From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 23:09:03 +1000 Sheyore Omovie wrote: I am doing

Re: [gmx-users] potential energy =nan

0 TER ENDMDL From: Sheyore Omovie [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 11:44:32 -0500 Hi Mark, I'm sorry, I assume you'll understand that I've

Re: [gmx-users] potential energy =nan

Martin's advice on making the water flexible. Rgds John From: Mark Abraham [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] potential energy =nan Date: Wed, 20 Jun 2007 23:09:03