Hi Pratibha, I can't think of a simple solution using Gromacs' tools. Sorry.
Cheers, Tsjerk On Mon, Aug 18, 2014 at 11:31 AM, pratibha kapoor <[email protected] > wrote: > Thanks Tsjerk for clearing my doubt. > Is there any other inbuild function which can serve my purpose? > > Thanks > Pratibha > > > > Hi Pratibha, > > > > Unfortunately, that is not going to work. trjorder puts the closest water > > molecule first in the output trajectory. But the closest one at time t > need > > not be the same as the closest one at time t+dt. So the MSD will be > > meaningless. > > > > Cheers, > > > > Tsjerk > > > > > > On Sun, Aug 17, 2014 at 11:20 AM, pratibha kapoor < > > [email protected] > > > wrote: > > > > > Hi users, > > > > > > I would like to calculate diffusion of water molecules in the first > > > hydration shell (say 0.4nm around protein). I have used trjorder > command > > > as: > > > trjorder -f *.xtc -s *.tpr -o ordered.xtc -r 0.4 > > > Can I directly use > > > g_msd -f ordered.xtc -s *.tpr > > > after that to calculate diffusion of water molecules closest to > protein? > > I > > > guess this would serve the purpose and there is no need to specifically > > add > > > n closest water in index group (Please correct me if I am wrong). But > > then > > > what does following line mean (line copied from trjorder -h): > > > > > > "When an index group of the first n waters is made, the ordered > > trajectory > > > can be used with any Gromacs program to analyze the n closest waters." > > > > > > Based on reading previous posts on the mailing list, I realise that for > > msd > > > calculation we have to use *.xtc with no pbc applied. In above case > won't > > > trjorder automatically uses pbc yes condition. In this regard, is it > > > reasonable enough to use ordered.xtc for msd calculation? > > > > > > Please reply. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
