Re: [gmx-users] Document about file input format to GROMACS program?

root wrote: Dear GROMACS user: We downloaded the AMBER-03* potential parameters files (ffamber_v3.3.1-doc.tar.gz) linked with the page http://folding.stanford.edu/ffamber/index.html#validation. We tried to simulate the Dickerson dodecamer using the 3.3.1 gromacs version. Our simulation crash wh

[gmx-users] Document about file input format to GROMACS program?

Dear GROMACS user: We downloaded the AMBER-03* potential parameters files (ffamber_v3.3.1-doc.tar.gz) linked with the page http://folding.stanford.edu/ffamber/index.html#validation. We tried to simulate the Dickerson dodecamer using the 3.3.1 gromacs version. Our simulation crash when we run the g

Re: [gmx-users] What are lines for g_sas -or file.xvg not g_sas -o file.xvg?

Arthur Roberts wrote: time hydrophobic-SAS hydrophilic-SAS total-SAS hydration-free-enthalpy is for: "g_sas -s mdrun.tpr -f mdrun.trr -o mdrun.xvg" not "g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg" There are only two lines in the xmgrace file. One is black. It is the larger number and

[gmx-users] What are lines for g_sas -or file.xvg not g_sas -o file.xvg?

time hydrophobic-SAS hydrophilic-SAS total-SAS hydration-free-enthalpy is for: "g_sas -s mdrun.tpr -f mdrun.trr -o mdrun.xvg" not "g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg" There are only two lines in the xmgrace file. One is black. It is the larger number and the other is red. It

Re: [gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

Arun kumar wrote: Hi Tsjerk and others, I tried to simulate one surfactant and one chloride ion in 500 waters and got similar type of errors. I mean my system got collapsed for l-bfgs minimization and for steepest descent the potential energy is a large number.(obviously some

[gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

of them may be > different. This is an issue, which has also been dealt with > extensively (including the past week). In any case, when reporting > that you've ran into a problem, it may be helpful to us to send your > .mdp file. > > Cheers, > > Tsjerk > > -- >

Re: [gmx-users] double-checking

V. Tanchuk wrote: Dear Users, I am trying to simulate Drug – Enzyme Complex accoring to "GROMACS Tutorial for Drug – Enzyme Complex" with different enzyme (ALKALINE PHOSPHATASE FROM HUMAN PLACENTA - ZEF1) and ligand. After adding water with genbox I run: grompp -f em.mdp -c trp_b4ion.pdb