RE: [gmx-users] a bit strange errors(Solved:Thanks to all)

om: xiaowu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 15:51:18 +0800 Dear Berk, In fact, I calculated the potential and force from the analytical function of angles in degrees, which is multicentred Gaussian-based potentials. So I

RE: [gmx-users] a bit strange errors

: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 09:39:07 +0200 Hi, But there could be a very similar issue there for the conversion from radians to degrees. The force has to be in units of kJ/mol/degree, not kJ/mol/radian. Berk

RE: [gmx-users] a bit strange errors

Hi, But there could be a very similar issue there for the conversion from radians to degrees. The force has to be in units of kJ/mol/degree, not kJ/mol/radian. Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 15:35

RE: [gmx-users] a bit strange errors

: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 09:21:18 +0200 Hi, Last week another user reported very similar problems (also 164% deviations, I think). In that case it seemed that the user did an Angstrom to nm conversion in the table file on x without scaling f(x). Could this

RE: [gmx-users] a bit strange errors

@gromacs.org Subject: RE: [gmx-users] a bit strange errors Date: Fri, 16 Oct 2009 14:55:40 +0800 Dear Mark, Thank you very much for the quick reply to my post. According to your suggestion, I check the table and reformat it with equal spacing between entries. I also check the entries calculated

RE: [gmx-users] a bit strange errors

given, which lead to terminate the simulation. Are there any other reasons responsible for it? Best wishes, Chaofu Wu, Dr. > Date: Fri, 16 Oct 2009 14:18:17 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] a bit strange errors >

Re: [gmx-users] a bit strange errors

wuxiao wrote: > Dear GMXers, >Recently, I has been performing coarse-grained MD simulations based > on the tabulated potentials using GROMACS. In the initialization, some > warnings are given as follows > /WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the > forces deviat

[gmx-users] a bit strange errors

Dear GMXers, Recently, I has been performing coarse-grained MD simulations based on the tabulated potentials using GROMACS. In the initialization, some warnings are given as follows WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the forces deviate on average 164% from m