[gmx-users] Cyclohexane as a solvent

[Dr. Vitaly Chaban]

if you prepare a separate ITP for each solvent, you will save some nerves
in the long term....



Dr. Vitaly V. Chaban


On Thu, Jul 11, 2013 at 7:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/11/13 8:59 AM, Shima Arasteh wrote:
>
>> Dear all,
>>
>> I see cyclohexane parameters in top & par CGenFF files. Would it be
>> correct if I add this molecule to the rtp file in charmm and then use it as
>> a solvent rather than for example water?
>>
>
> The .rtp mechanism is generally used for building blocks of larger
> molecules, for which topologies are built with pdb2gmx.  There's nothing
> wrong with building an .rtp, but it's probably about the same work as
> building an .itp, and then you have to run pdb2gmx and modify the topology
> it gives you (from .top to .itp).  Save some work and just write the .itp
> file, especially since you already have all the parameters.
>
>  Generally, how is it possible to add a new solvent to the charmm ff
>> simulations?
>>
>>
> Like you would any other standalone molecule - write an .itp for it.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Associate
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> 706-7441
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