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 listgmx-users@gromacs.or
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 pinst
romacsWrapper/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-Ju
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 simulation
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 valu
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