[gmx-users] Colchicine topology

Soham Sarkar soham9038 at gmail.com
Mon May 28 11:23:51 CEST 2018

Dear All,
               I have a simulation box of dimension 8*6*4 nm3. The center
of the box is the center of the two center of masses of two ss-DNA. I want
to calculate the 2D distribution of the ions surround the strands in the
box. I chose Chain_A, Chain_B and ion as three groups, rather I am confused
with the options that should be added to have the correct dimension of the
finally produced image. what argument I should add for -amax and -rmax?
Anything else I have to use in the command line? The colour is also not
shown , what is the reason? can anyone please tell me
Thanks in advance

On Mon, May 28, 2018 at 1:04 PM, Alex <nedomacho at gmail.com> wrote:

> That's not my intention - someone seeking a topology would do well to a)
>> know the past research to inform their decisions, including whether to
>> repeat deliberately, and b) also ask them to share input files.
>> I was obviously joking, not to derail this thread. Besides, in
> biomolecular fields, FF development in general and topology building in
> particular, you guys have at least some unity in how to approach things. In
> solid state (or solid-liquid systems), we have a pretty arbitrary zoo. The
> cherry on top of this cake is recent OPLS-AA-based FF for two widely
> studied nanomaterials with partial charges coming from DDAP, which is
> entirely different from CHELPG used for OPLS originally. And everything
> fits everything!
>> A lot of past work is horrible, yes :-)
>> Always!
> Alex
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Junior Research Fellow
Department of Chemistry

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