Hi,
If you want to get it
go here(if you are luck)
http://www.gromacs.org/contributed_by_users/task,cat_view/gid,39/
If you want to make one
go here
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
If you want to learn how to make then get here
Hi,
I am trying to calculate free energy and diffusivity of a guest
molecule at a given height from lipid bilayer. I am using pull code
with runtype=constraint, reftype=com, pulldim=N N Y
in version 3.3.1 compiled in double precision. The ensemble is NPT
(Nose-Hoover/ Parrinello-Rahman).
To save
Hi, Mark, thanks for your reply.
After some efforts I have been successful to insert potassium using ff
oplsaa. But it seems that ff g43a1 actually can not recognize K or K+.
It doesnt matter, anyway I can select ff oplsaa.
Zhongqiao Hu
Lab E5-04-27
Tel: 65161946(O)
Department of Chemical
Besides used for h-bond, g_hbond can be used for determine whether the
distance has fallen into a range (with -nocontact and -r and -r2).
g_dist is not good for calculate for distance between two atoms but
g_mindist can perform this job well. Actually, because of a compulsive
input of tpr
Hi all,
Now I meet a problem when building a system. I used prodrg to get the .pdb
of a single molecule, write the .top file manually. The single-molecule
system is equilibriumed (em, NVE, NTV,NTP are all ok for at least 1 ns).
Then I used two method to get a bigger (8 molecules) system: 1)
Qiao Baofu wrote:
Hi all,
Now I meet a problem when building a system. I used prodrg to get the
.pdb of a single molecule, write the .top file manually. The
single-molecule system is equilibriumed (em, NVE, NTV,NTP are all ok for
at least 1 ns). Then I used two method to get a bigger (8
Hi Tsjerk,
Thanks for helpful advice. I decided to re-build my system from scratch, and I
ran energy minimization again. This still ended badly, with a potential energy
on the order of 10^8. Better than 10^18, but still not anywhere close to
acceptable.
My guess is that you've generated
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