Hi gmx users,
I'm trying to create an equilibrated 2,3 dihydroxynaphthalene solvent box. I
used PRODRG2 server to create an itp file from the
downloaded pdb file. I used genbox to insert the solvent randomly into a 5
nm cubic box. Then I energy minimised it and did NVT and NPT equilibration
on
On 6/11/12 6:42 AM, Satish Kamath wrote:
Hi gmx users,
I'm trying to create an equilibrated 2,3 dihydroxynaphthalene solvent box. I
used PRODRG2 server to create an itp file from the
downloaded pdb file. I used genbox to insert the solvent randomly into a 5
nm cubic box. Then I energy
Hi dear all
I'm simulating a system containing CNT, when I put CNT in a unit cell and want
to run energy minimization in a vacuum, I encounter with such an error: The
optimal PME mesh load for parallel simulations is below 0.5 and
for highly parallel simulations between 0.25 and 0.33, for
Hi
I am still stuck with same problem of obtaining positive potential energy.
On 11/11/2011 5:07 PM, Harpreet Basra wrote:
Hi
I am trying to generate an equilibrated box of 216 TFE molecules.To
generate the 216 TFE molecule box i performed following steps:
A suggested workflow can be found
On 15/11/2011 6:06 PM, Harpreet Basra wrote:
Hi
I am still stuck with same problem of obtaining positive potential
energy.
On 11/11/2011 5:07 PM, Harpreet Basra wrote:
Hi
I am trying to generate an equilibrated box of 216 TFE molecules.To
generate the 216 TFE molecule box i performed
On 11/11/2011 5:07 PM, Harpreet Basra wrote:
Hi
I am trying to generate an equilibrated box of 216 TFE molecules.To
generate the 216 TFE molecule box i performed following steps:
A suggested workflow can be found here
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
1) I
Hi
I am trying to generate an equilibrated box of 216 TFE molecules.To
generate the 216 TFE molecule box i performed following steps:
1) I got the tfe.gro file and created a cubic box of edge length =
0.516 nm containing 1 TFE molecule (at its center), using the
following command:
editconf -f
Dear all,
This may sound obvious and normally I would know how to address the
following question. However, I would like to ask for your opinion.
If we are simulating bulk liquid of hydrocarbon using the shell
polarizable model, is it possible to have a positive value for the
potential energy?
On 2011-02-27 21.20, aldi asmadi wrote:
Dear all,
This may sound obvious and normally I would know how to address the
following question. However, I would like to ask for your opinion.
If we are simulating bulk liquid of hydrocarbon using the shell
polarizable model, is it possible to have a
Many thanks David.
Just want to confirm that I understand how to calculate the monomer
correctly. So I put the single molecule inside a large cubic box, say
with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the
same cut-off parameters as the ones that I apply during my bulk
On 2011-02-27 21.49, aldi asmadi wrote:
Many thanks David.
Just want to confirm that I understand how to calculate the monomer
correctly. So I put the single molecule inside a large cubic box, say
with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the
same cut-off parameters as
Hi,
I am running a carbon nanotube in water simulation. I set the
reaction field dielectric constant (epsilon_rf) to 80 (that of water)
and the dielectric constant (epsilon_r) to 1. The energy minimization
(which ignores the temperature coupling) runs well and I get a negative
potential
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