[gmx-users] Extracting enthalpies during or after MD

Hello, I am wondering if it is possible to output interaction energies/enthalpies during an MD simulation between specific groups of atoms. The energies are all calculated anyways before the forces are calculated, so I am wondering if there is an option to output those energies to a file? I saw

Re: [gmx-users] Extracting enthalpies during or after MD

Hi Mark, Thanks for the quick reply. The thing with the energy groups makes sense now. But I have run into another problem with the method... The same atom cannot be in multiple energy groups during a simulation. Let say that I want the interaction energy between water and lipid head-group and

Re: [gmx-users] Extracting enthalpies during or after MD

Thanks for the help Mark. Just to make sure I understand you correctly, I have a few comments/questions, see below... kind regards, Jesper > - Original Message - > From: li...@jsx.dk > Date: Friday, June 4, 2010 10:35 > Subject: Re: [gmx-users] Extracting enthalpies during or after MD > T

Re: [gmx-users] Extracting enthalpies during or after MD

Aaah, I get it now (finally)... Thanks again... Jesper > > > - Original Message - > From: li...@jsx.dk > Date: Saturday, June 5, 2010 5:58 > Subject: Re: [gmx-users] Extracting enthalpies during or after MD > To: Discussion list for GROMACS users > >> Thanks for the help Mark. Just to ma

[gmx-users] g_energy output

Dear all, I have run a CG-MD simulation and output energies of different energy groups. When I run g_energy to get some of the energy terms out I input the number of molecules in my system -nmol "X" (X = Y number of water molecules (beads) + Z number of proteins + W number of lipids), to make sure

Re: [gmx-users] Energy profile with umbrella sampling

On 7/10/06, [EMAIL PROTECTED] <[EMAIL PROTECTED] > wrote: From: "Robert fiske" <[EMAIL PROTECTED] >Subject: [gmx-users] Energy profile with umbrella samplingWe are using umbrella sampling to observe a hydrogen transfer.  And wouldlike to analyze our results by graphing the energy against the reacti

[gmx-users] Re: g_energy average --- bug?

From: pim lists <[EMAIL PROTECTED]>Date: Mar 2, 2006 12:17 PMSubject: Re: g_energy average --- bug? To: gmx-users@gromacs.orgDate: Thu, 2 Mar 2006 10:49:38 +0100 From: "Fernando Mattio" < [EMAIL PROTECTED]>Subject: [gmx-users] g_energy average --- bug?    However, the a