Re: [gmx-users] dynamics with toluene as solvent

I think you can use The Dundee PRODRG sever to generate toluene structure and topology for gromacs, but use it with care. On 9/21/07, Eva Santos <[EMAIL PROTECTED]> wrote: > > > Hello everyone, > > I need to do some molecular dynamics, using gromos96 force field, with > toluene as solvent. > I ha

Re: [gmx-users] g_rdf in fedora core 5

root wrote: I compiled and installed gromacs 3.3.1 in Fedora Core 5 using gcc 4.1.0, now,when I want to use it ,it always displays "Reading frame0 time 0.000". Does anyone have the same problem with me? Is there any method to solve the problem? Thanks very much in advance. _

[gmx-users] g_rdf in fedora core 5

I compiled and installed gromacs 3.3.1 in Fedora Core 5 using gcc 4.1.0, now,when I want to use it ,it always displays "Reading frame0 time 0.000". Does anyone have the same problem with me? Is there any method to solve the problem? Thanks very much in advance. ___

RE: [gmx-users] g_energy -fee -inf problem

Thanks Mark for pointing out my error. I will do it accordingly. With best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTE

Re: [gmx-users] g_energy -fee -inf problem

Naser, Md Abu wrote: Hi Mark, The reacton shuld occur as: R-S-S-R + 2H+ -> 2R-SH. So at the very least, your "after" topology will need to have these hydrogens... You can't just cleave the S-S bond out of the .top and expect it to work. Mark

RE: [gmx-users] g_energy -fee -inf problem

Hi Mark, The reacton shuld occur as: R-S-S-R + 2H+ -> 2R-SH. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] o

Re: [gmx-users] g_energy -fee -inf problem

Naser, Md Abu wrote: Hi Mark, Thank you very much for your replay.I was just trying to calculate free energy difference between reduced protein and non-reduced protein solvated in water(spc) using ffG43a2 force field. OK, so other than bond cleavage, what happens to the sulfurs when you reduc

RE: [gmx-users] g_energy -fee -inf problem

Hi Mark, Thank you very much for your replay.I was just trying to calculate free energy difference between reduced protein and non-reduced protein solvated in water(spc) using ffG43a2 force field. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PR

RE: [gmx-users] atom index number

Hi Erik, Thank you very much for responding my query. I will try doing it using grep, awk and cut. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Me