Re: [gmx-users] Re: Frame/conformation in trajectory is ignored

On Fri, Jul 15, 2011 at 1:41 PM, Mark Abraham wrote: > ** > On 15/07/2011 7:31 PM, Martin Kamp Jensen wrote: > > Hello, > > I am trying to evaluate energy values of several conformations using a > (pseudo)trajectory. Currently, I am concatenating GROMOS-96 files (.g96) and > using that as a traje

Re: [gmx-users] Re: Frame/conformation in trajectory is ignored

On 16/07/2011 8:33 PM, Martin Kamp Jensen wrote: On Fri, Jul 15, 2011 at 1:41 PM, Mark Abraham > wrote: On 15/07/2011 7:31 PM, Martin Kamp Jensen wrote: Hello, I am trying to evaluate energy values of several conformations using a (pseudo)traject

[gmx-users] General Question about Simulated Annealing

Hello all, I have read many papers about using simulated annealing protocol along with experimental data. I have some questions about the protocol itself and would really appreciate if some body clears it. The general MD simulation gets the information about forces from FF and starting with initi

Re: [gmx-users] General Question about Simulated Annealing

On 17/07/2011 2:13 AM, santhu kumar wrote: Hello all, I have read many papers about using simulated annealing protocol along with experimental data. I have some questions about the protocol itself and would really appreciate if some body clears it. The general MD simulation gets the informat

[gmx-users] reg SMD and h-bonding

Dear justin ,    Thank you  for your previous reply. Can i correlate difference in  pullf.xvg profiles for various concentration of salt . I mean can i compare Pullf.xvg profile and H-bonding strength is there is any relation exists ? will maxima of pullf.xvg depends on H-bondin

Re: [gmx-users] reg SMD and h-bonding

vidhya sankar wrote: Dear justin , Thank you for your previous reply. Can i correlate difference in pullf.xvg profiles for various concentration of salt . I mean can i compare Pullf.xvg profile and H-bonding strength is there is any relation exists ? will maxima of pullf.

[gmx-users] Poisson-Boltzmann free energy in gromacs?

Hi, I was wondering whether, in gromacs, there is any way of calculating the electrostatic free energy using poisson Boltzmann equation. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs

Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?

Sanku M wrote: Hi, I was wondering whether, in gromacs, there is any way of calculating the electrostatic free energy using poisson Boltzmann equation. There is no mention of such a feature in the manual, so I would suspect the answer is no. -Justin -- ===

Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?

I thought since the implicit solvent model has been invoked recently, there might be some features for PB calculation as well. From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Sat, July 16, 2011 7:35:43 PM Subject: Re: [gmx-users] Poisson-Bol

Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?

Sanku M wrote: I thought since the implicit solvent model has been invoked recently, there might be some features for PB calculation as well. You can get GB polarization energies with the implicit solvent code, but not PB, as far as I am aware. If there are undocumented features, perhaps

Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?

On 17/07/2011 10:45 AM, Justin A. Lemkul wrote: Sanku M wrote: I thought since the implicit solvent model has been invoked recently, there might be some features for PB calculation as well. You can get GB polarization energies with the implicit solvent code, but not PB, as far as I am awa