[gmx-users] polymer NVT

David van der Spoel spoel at xray.bmc.uu.se
Sat Jul 23 09:10:31 CEST 2005

On Fri, 22 Jul 2005, javier wrote:

>Dear Gromacssss
> My system consist of 1 polymer chain, and I need to do NVT simulations, so
>I need to fix the box size according to  my polymer density.
> But I really do not understand editconf?
>My edit conf is: ediconf -bt cubic -f file.gro -o out.gro -d 0.5 -center
>But in this way I do not get the right density, so I have tried:
>ediconf -bt cubic -f file.gro -o out.gro -d 0.5 -density 1010
>but the resulting  box vector lengths are a=4 b=7 and c=0.3.  Therefore I
>only can use very small cutoffs due to the small c value.
>And my polymer chain does not look like a Gaussian chain, and it is outside
>of the cell.
>So, do you have some idea?

make a box of 7 7 7 that fits the chain
do a simulation with pressure coupling to 100 bar and watch the box 
contract. then do sim with pressure 1 bar and check the final density. If 
it is not right check your force field.

you need pbc = full for this kind of simulation (and constraint algorihtm 
LINCS with CVS code or no constraints with 3.2.1).

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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://xray.bmc.uu.se/~spoel

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