Dear all,
I’ve a doubt/question. I ran a long simulation of my system (100ns) at 298K.
Now I want to see the effect of the T on my system and I want to run a 20ns
simulation at 350K and 400K, now my question is: Do I have to run this
simulation under the NPT condition or under the NVT (using an
Hi,
I am including position restraints as one of the directives under
[moleculetype] (as shown on page 137 (section: 5.7, manual:4.6.4 pdf)).
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
;i j k l func phase kd
On Wednesday, January 1, 2014 at 6:33 PM, Tom dna...@gmail.com wrote:
Can someone help us about how to add misssing parameters
into Topolbuild?
We are using topolbuild to build *top file for a molecular which
has amide group.
Topolbuld reports missing parameters of bonding, angle and
On 1/2/14, 6:41 AM, Chetan Mahajan wrote:
Hi,
I am including position restraints as one of the directives under
[moleculetype] (as shown on page 137 (section: 5.7, manual:4.6.4 pdf)).
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
;i
Hi all,
The system I'm working with is Protein G (ID: 1PG) with a graphene surface
using Implicit Solvent.
I perform an energy minimization using steepest descent with 1000 steps and
0.001 ps time step. Then I use simulation annealing for 200ps to heat the
system to 300K.
After heating, the
Hi,
Can I insert the other force fiels such as COMPASS to GROMACS? Thanks for
anyone's help.
Best regards!
Zhicheng
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