[gmx-users] using implicit water for atomistic simulation of lipid bilayer

2016-12-09 Thread Mohsen Ramezanpour
Dear Gromacs Users, I was wondering if there is any example of using Implicit water model for lipid bilayers in Gromacs? I have read on using implicit solvents in Gromacs and found interesting discussions: https://groups.google.com/forum/#!topic/archive-gmx-users/0HIFVop390I https://mailman-1.s

Re: [gmx-users] xtc to dcd conversion

2016-12-09 Thread Justin Lemkul
On 12/9/16 1:35 AM, Amir Zeb wrote: Hi How can I convert xtc file of trajectory to dcd file for dccm analysis? catdcd can do this. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutic

Re: [gmx-users] static compilation - various problems...

2016-12-09 Thread Mark Abraham
Hi, On Sat, Dec 10, 2016 at 5:43 AM Krzysztof Piszczek < krzysztof.piszc...@boincpolska.org> wrote: > Hello, > Firstly, I'm introduce myself. > I'm BOINC administrator for few projects and if one of them we would > like to use gromacs as application for volunteers. > Basic requirement is that app

[gmx-users] static compilation - various problems...

2016-12-09 Thread Krzysztof Piszczek
Hello, Firstly, I'm introduce myself. I'm BOINC administrator for few projects and if one of them we would like to use gromacs as application for volunteers. Basic requirement is that applications have to be fully static as we don't wan't to push volunteers to compile and/or install full gromacs. I

[gmx-users] About surface in GROMACS

2016-12-09 Thread Faust SHI
Hi, Does anyone know about if I can create only one surface in GROMACS? I can make two now by increasing the box size of one dimension but don’t know how to get only one. Thanks, Faust -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/G

[gmx-users] Calculating osmotic coefficient through virial/kinetic terms: what is the handy way?

2016-12-09 Thread Vries, de, H.W.
Dear all, I am trying to find the osmotic coefficient of a set of ions in an implicit solvent system in gromacs 4.5.3. I have found multiple papers reporting an expression of the form: Osm. coefficient = 1- (Virial/Ekinetic). I can find in the manual (appendix B) how the single sum virial is com

[gmx-users] Query regarding hydrogen bond lifetime and energy

2016-12-09 Thread Apramita Chand
Dear All, Is there any way to calculate hydrogen bond energy in GROMACS ? Or at least any information which could be applied from GROMACS to calculate the energy. Also,let me repeat my earlier query. I'm trying to calculate the hydrogen bond lifetime in my system (water-ethanol) using command g_h

Re: [gmx-users] material science

2016-12-09 Thread Mark Abraham
Hi, It sounds like you could benefit from some background learning about molecular modelling - even that wikipedia page is pretty good :-) Mark On Fri, Dec 9, 2016 at 8:19 PM RAHUL SURESH wrote: > what ispairwise potentials? > What's EAM.? > > -- > *Regards,* > *Rahul Suresh* > *Research Schol

[gmx-users] material science

2016-12-09 Thread RAHUL SURESH
what ispairwise potentials? What's EAM.? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.

[gmx-users] How to use Höltje's cholesterol parameters ?

2016-12-09 Thread Sim gmx
Hello everyone, I am currently working on interactions between small biomolecules and bilayers. Phospholipids parameters come from Peter Tieleman's website (Berger lipids forcefield) and the small compounds are parametrized for gromos53a6. I would like to add cholesterol to my bilayers, which is v