On 7/9/12 4:07 PM, SatyaK wrote:
Hello,
I followed below steps using VMD and GROMACS but something went wrong in
using GROMACS which I am not able to figure out. Appreciate your help.
1. editconf -f initialfile.pdb -o initialfile.gro -d 0.2
2. VMD: within 5 of nucleic
On 07/05/2012 01:04 PM, SatyaK wrote:
Thanks once again Mark. I am trying to figure out things. Basically, I am
using ReaxFF for my simulations.
Has that been ported to GROMACS? If not, you have that issue to consider
first.
The basic problem I want to address is, to
place OH radicals
Hi Satya,
You can use trjorder to rearrange solvent molecules in your structure
file, according to distance. Then you can replace the first x solvent
molecules by hydroxyl. Actually you only need to remove a hydrogen
atom per water...
Hope it helps,
Tsjerk
On Thu, Jul 5, 2012 at 5:04 AM,
Uhmm, you remove particles, modify molecule types, and wonder whether
there is continuity in the trajectories?
Ah well, let's say you were to do a simulation and at some point t you
suddenly have some hydrogen atoms that have lost all interaction with
the system, and on top of that have the
On 5/07/2012 12:28 AM, SatyaK wrote:
Thanks Mark for your response. These are steps I followed to construct
DNA+Water molecules.
editconf -f A.pdb -o A.gro -d 0.3
genbox -cp A.gro -cs -nice -20 -o A_water.gro
That's not going to achieve your objective. I gave you a
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