[gmx-users] Charges in vacuum simulation

Hi all, I'm trying to run a vacuum simulation of my protein which has a non-zero charge. How to deal with this charge? Can I add counter ions in to my system? Would it be energetically stable? How can one bring a protein to its isoelectric point? -- gmx-users mailing list

Re: [gmx-users] Testing the performance of

Thanks! Mark. I got solution to my problem. For my system, setting pinoffset = 0, 16 and pinstride = 1 for two simultaneous simulations gave much satisfactory performance both for Verlet and Group cutoff-scheme. I tried it for 4 simultaneous simulations also with pinoffset = 0, 8, 16, 24 and

Re: [gmx-users] TRACE OF RMSD COMPARISON MATRIX

might be helpful: http://orbeckst.github.io/GromacsWrapper/gromacs/core/fileformats/xpm.html -g -- Gaurav Goel Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India On 02-Jul-2013, at 10:45 AM, Richa Singh

[gmx-users] Testing the performance of

Hello, I want some inputs on observed performance of protein-in-water simulations run on a single server with 2 Intel Xeon E5-2660 processors. Each processor has 8C/16T, so total 16C/32T. My system is composed of 1643 beta-microglobulin atoms and 24699 water atoms. I ran several 500ps

[gmx-users] TRACE OF RMSD COMPARISON MATRIX

Hello users, I'm using g_rms to compare my actual trajectory obtained from simulation with the filtered trajectory (along given set of eigenvectors), this gives me an RMSD comparison matrix in xpm format where the values of the plot are not clear. Is there any way which can help me to get the