[gmx-users] Regarding msd
jalemkul at vt.edu
Wed Oct 8 13:29:44 CEST 2014
On 10/8/14 3:21 AM, rajat desikan wrote:
> You need to use -pbc nojump to calculate the msd. Using -pbc whole is wrong
> for calculating the msd.
Upon what do you base this statement? I get identical results with an
unprocessed trajectory, and those treated with either -pbc whole or -pbc nojump.
> On Tuesday, October 7, 2014, pratibha kapoor <kapoorpratibha7 at gmail.com>
>> Hi all
>> I have created my own code for msd calculation and would like to verify it
>> from g_msd. I have created pdb files using trjconv -center -pbc whole
>> option. Can I use the coordinates in pdb as such (with no
>> wrapping/unwrapping/shifting) for running my code? or does the inbuild
>> g_msd program modifies them (shift)?
>> My msd values are not matching with the g_msd values. I suspect that
>> discrepency in the pdb file creation since the values obtained from my
>> program agrees with manual calculation (of some dummy values).
>> Any suggestions are highly welcomed.
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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