[gmx-users] Regarding msd

Justin Lemkul jalemkul at vt.edu
Wed Oct 8 13:29:44 CEST 2014

On 10/8/14 3:21 AM, rajat desikan wrote:
> Hi,
> 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>
> wrote:
>> 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
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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