[gmx-users] toluene as a slovent

[David van der Spoel]

Den 2019-12-02 kl. 17:10, skrev Mijiddorj B:
> I recommend you to use (1) gmx insert-molecules tool to fill the box that
> solvent molecule. For the number of molecules, you can use as much as a
> higher number using -nmol option. The result tells you, how many molecules
> inserted from ordered numbers. (2) Then, you should manually edit the
> topology file using the correct number of toluene.

http://virtualchemistry.org/molecule.php?filename=toluene.sdf
http://virtualchemistry.org/ff.php
> 
> 
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Mon, 2 Dec 2019 12:14:21 +0330
>> From: Iman Katouzian <imaneternity at gmail.com>
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: Re: [gmx-users] toluene as a slovent
>> Message-ID:
>>          <CALipc=ovOtQ9Fq0SXpBRoe=
>> ffcoDUoQOGukzUUwcb_+tAmOOpw at mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Hello,
>>
>> I have downloaded the toluene pdb file and want to use it as solvent in
>> GROMACS rather than the water molecules. I have added toluene as a molecule
>> using gmx solvate -cs toluene.gro however, in the next steps, it is not
>> added to the topol.top file and I cannot go-ahead to the next steps of
>> simulation. I'd be grateful if someone can help me with this issue as I
>> have not tried other solvents rather than water before.
>>
>> Thanks.
>>
>> On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian <imaneternity at gmail.com>
>> wrote:
>>
>>> Hello,
>>>
>>> I have downloaded the toluene pdb file and want to use it as solvent in
>>> GROMACS rather than the water molecules. I have added toluene as a
>> molecule
>>> using gmx solvate -cs toluene.gro however, in the next steps, it is not
>>> added to the topol.top file and I cannot go-ahead to the next steps of
>>> simulation. I'd be grateful if someone can help me with this issue as I
>>> have not tried other solvents rather than water before.
>>>
>>> Thanks.
>>>
>>> --
>>>
>>> *Iman Katouzian*
>>>
>>> *Ph.D.** candidate of Food Process Engineering*
>>>
>>> *Faculty of Food Science and Technology*
>>>
>>> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
>>>
>>
>>
>> --
>>
>> *Iman Katouzian*
>>
>> *Ph.D.** candidate of Food Process Engineering*
>>
>> *Faculty of Food Science and Technology*
>>
>> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
>>
>>
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>>
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>> End of gromacs.org_gmx-users Digest, Vol 188, Issue 3
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se