Re: [gmx-users] Illegal instruction flag raised in GMX 5.0.4

2014-12-23 Thread Harry Mark Greenblatt
BSD Gromacs is telling you that the -h option you supplied is not valid for this command. You can see all the valid arguments for each command here http://manual.gromacs.org/online.html Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology

Re: [gmx-users] Illegal instruction flag raised in GMX 5.0.4

2014-12-23 Thread Carsten Kutzner
Hi there, On 23 Dec 2014, at 08:59, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Gromacs is telling you that the -h option you supplied is not valid for this command. No, that is not true, the -h option works for all Gromacs commands. It is exactly this option that

[gmx-users] malloc error at mdrun step

2014-12-23 Thread Kalyan Reddy
Dear Users, I am learning free energy calculations using MD (Desolvation free energy of Methane in water) from Justin Lemkul's tutorials. For this I have installed gromacs-5.0.1 version on my Mac Pro workstation and proceeding with the calculations as mentioned in the tutorials. When I ran mdrun

[gmx-users] Implicit and explicit solvation

2014-12-23 Thread neha bharti
Hello all Can any one please tell me What is Implicit and explicit solvation?? And Which kind of solvation is used in Justin A. Lemkul tutorial?? With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Implicit and explicit solvation

2014-12-23 Thread Erik Marklund
Dear Neha, Wikipedia (or any simulation textbook) can! http://en.wikipedia.org/wiki/Implicit_solvation Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road

Re: [gmx-users] Illegal instruction flag raised in GMX 5.0.4

2014-12-23 Thread Mark Abraham
... and see http://www.gromacs.org/Documentation/Installation_Instructions#portability-aspects Mark On Tue, Dec 23, 2014 at 7:25 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi there, On 23 Dec 2014, at 08:59, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Gromacs is

Re: [gmx-users] Protein split with mindist

2014-12-23 Thread Tsjerk Wassenaar
Hi Jinxin, Better try trjconv -pbc whole trjconv -pbc nojump should work if your protein is whole (and matching) in the reference structure. Fittings screws up the PBC. Cheers, Tsjerk On Dec 23, 2014 6:02 AM, jinxin 18819028...@163.com wrote: Hi Tsjerkthank you very much ! as you said,

[gmx-users] calculation of H-bonds

2014-12-23 Thread soumadwip ghosh
Dear all, my project involves around the interaction of DNA with small molecules. I want to calculate (rather show) the native H-bond breaking of a double stranded DNA in the presence of three ions. Some of my ions are capable of making secondary H bonds and I want to show that as

[gmx-users] Error in topology using g_x2top

2014-12-23 Thread Rajan Kumar
Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of Hydroxyl and epoxide group on only one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. Since my simulation

[gmx-users] Pulling code

2014-12-23 Thread asasa qsqs
Dear Justin A. Lemkul, I want to use pulling code for calculate the PMF of a molecule at the across the DMPC, but i can't obtained a large pull across the membrane my pulling code was: ; Pull code pull= umbrella pull_geometry= position pull_dim= N N Y pull_start = yes; define