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
$s
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
$sel writepdb initialfile_updated.pdb
Hello Tsjerk,
I followed below steps to create a box with DNA and water molecules that
are close to it at some distance:
1. g_select -s Test.gro -select '"Close to A" resname SOL and within 0.5 of
resname A' -on
(since I need around DNA molecule, I randomly chose residue A, such that
wate
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 nature
Hello Tsjerk,
I was wondering, once we order the water molecules and place Oh radicals in
the system, do we loose the continuity of their trajectories when we run
the simulations using Lammps?
With Regards,
Satya.
--
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http://gromacs.5086.n6.nabble.com/DNA-simu
Thanks Tsjerk for your guidance. In fact, I had been removing some H atoms
from the water molecules (which are close to DNA by choosing them manually
depending on the coordinates which is a tedious process) to convert them to
OH. Then, I try to input this file to Lammps applying Reaxff potential.
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, Satya
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 a
Thanks once again Mark. I am trying to figure out things. Basically, I am
using ReaxFF for my simulations. The basic problem I want to address is, to
place OH radicals as close as possible to the DNA and rest with water
molecules in a box.
Thanks,
Satya.
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htt
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 workf
Thanks Mark for your response. These are steps I followed to construct
DNA+Water molecules.
> editconf -f A.pdb -o A.
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