On 2010-11-27 23.54, Apoorv Kalyankar wrote:
Hi,
I was wondering how does a thermostat work in a Non Equilibrium
Simulation(NEMD) in GROMACS.
Does it subtract out the streaming velocity before applying the
thermostat or does it not apply thermostat at all in
the direction of the applied
dear all,
I am doing a simluation that I want to fix the center of mass of
three protein chains , so that they don`t move to much away , should I fix
center of mass of every chains, or fix residues that most close to COM. what is
the diffenerces between the two method? and if I want
On 28/11/2010 4:49 AM, Sai Pooja wrote:
Hi,
I am running a script that uses mdrun of gromacs and does replica
exchange (not using -replex). The reason is that I want to use
different table files for different replicas. However, it seems that I
cannot supply unique table names. For example, if
Dear Justin,
Thanks for your reply.
I have checked whole pdb file. Everything is fine.
When I remove phosphorylated serine and use only serine then every thing
went fine.
co-ordinates for phosphoserine are as per following
ATOM 1684 N SEP X 167 27.040 22.580 8.280 1.00
0.00
ATOM
4 matches
Mail list logo