[gmx-users] density off
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 20 20:39:08 CEST 2011
On 2011-04-20 20.10, Juliette N. wrote:
> Hi David,
> I used to apply NPT to fix the density, how can I get the denisty using NVT?
You turn off P coupling and fix the right density by scaling using editconf.
> On 20 April 2011 13:46, David van der Spoel <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
> On 2011-04-20 19.40, Juliette N. wrote:
> I am trying to obtain the density for my system that is exactly
> identical to experimental value but whatever pressure I apply
> density is
> still off by 3%.
> Is this issue common?
> Jennifer N.
> Yes, force fields are not perfect.
> How about running NVT at the experimental density and measuring the
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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> Jennifer N.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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