Re: [gmx-users] Help with Principal component analysis

On 3/01/2012 6:54 AM, Alex Jemulin wrote: Dear all I run a MD on a GPCR (transmembrane protein) Then I run a PCA on results and I found 3PC sufficient to explain variance. On the same PC I get big values for samples located both at Nter (extracellular) and Cter (intracellular) or for similar ca

[gmx-users] free energy and charges

Dear GMX users, when I want to correct charge group of one molecule I have to do calculate its free energy. I did this work by applying 6th gromacs tutorial. In this tutorial user has to assign 0 value in topology: [ atoms ] ; nr type resnr residue atom cgnr charge mass type

Re: [gmx-users] Obtain the flux of water

On 31 Dec, 2011, at 21:50, Saeid Akbarshahi wrote: > Whether there is a program in Gromacs that would directly or indirectly > obtained the flux of water ? > > How to obtain the flux water in Gromacs ? A (long) while back I wrote g_count and g_flux, which are primarily useful for looking at f

[gmx-users] Help with Principal component analysis

Dear all   I run a MD on a GPCR (transmembrane protein) Then I run a PCA on results and I found 3PC sufficient to explain variance. On the same PC I get big values for samples located both at Nter (extracellular) and Cter (intracellular) or for similar cases such as both Nter(extracellular) and L

Re: [gmx-users] Reg: Langevine Thermostat

On 2/01/2012 11:37 PM, Rohit Farmer wrote: Hi guys ... Happy New Year Does anyone know how to use Langevine Thermostat in gromacs. Yes, but this is a very general question. I answered it on 23 Dec in a very general way. If you want more help, then you should be prepared to show you're worki

[gmx-users] Reg: Langevine Thermostat

Hi guys ... Happy New Year Does anyone know how to use Langevine Thermostat in gromacs. Thanks Rohit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before p