[gmx-users] X.gro file for different solvent system
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jan 28 07:51:51 CET 2008
kinshuk at chem.iitb.ac.in wrote:
> Hi all,
> I have a query regarding making .gro file for different solvent system.
> In SPC216.gro & MeOH.gro there is 216 water/MeOH molecules are there.In
> dmso.gro 208 molecules are there.In urea+h2o.gro 36 urea & 357 water
> molecules are there with particular box size.I couldn't understand what is
> the basic logic behind that?
no logic needed.
> I have to make the solvent system of guanidium ion + thiocynate ion +
> Water molecule.I have to use different box size & different
> concentration (6molal,7 molal).So how will i judge how many ions & water
> molecule in the X.gro file like urea+h2o.gro.Is it a particular ratio
> between urea & water molecules for particular concentration ? If it is
> then this X.gro file (guanidium + thiocynate ion + water ) will be input
> for -cs flag in genbox for particular concentration in different size of
> Kinshuk Raj Srivastava
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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