Liu, Liang wrote:
Well my first question is: if the pdb2gmx command must take a force
file? I guess it should be necessary. Then the available list contains
amber and others, but not user-specified potential. This will affect the
future simulation or calculation?
Yes. Gromacs allows you
Well my first question is: if the pdb2gmx command must take a force file? I
guess it should be necessary. Then the available list contains amber and
others, but not user-specified potential. This will affect the future
simulation or calculation?
On Thu, Nov 17, 2011 at 10:06 AM, Justin A. Lemkul
Liu, Liang wrote:
Well, I already have the xvg files from others. However I don't know how
to use it.
Start with the manual, where modifications to the topology and relevant commands
and files are described. Then refer to the how-to online, which has specific
instructions. Then, ask spe
Well, I already have the xvg files from others. However I don't know how to
use it.
On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Dear all,
>>
>> I am trying to calculate potentials for RNA structures with a serial of
>> tabulated potentials (non-bonded).
Liu, Liang wrote:
Dear all,
I am trying to calculate potentials for RNA structures with a serial of
tabulated potentials (non-bonded).
And the only potential I am going to use is the tabulated potentials,
and the effect from force field should be removed.
However, when I use pdb2gmx to build
Dear all,
I am trying to calculate potentials for RNA structures with a serial of
tabulated potentials (non-bonded).
And the only potential I am going to use is the tabulated potentials, and
the effect from force field should be removed.
However, when I use pdb2gmx to build the topology file, I ha
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