.
- Original Message -
From: "Justin Lemkul"
To: gmx-us...@gromacs.org
Sent: Tuesday, November 4, 2014 7:45:39 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On 11/4/14 12:45 AM, Nathan K Houtz wrote:
Thanks for your reply. However, I'm still confused
hanks again in advance - I really appreciate the help!
N.H.
- Original Message -
From: "Justin Lemkul"
To: gmx-us...@gromacs.org
Sent: Tuesday, November 4, 2014 7:45:39 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On 11/4/14 12:45 AM, Nathan K Houtz wrote
On 11/12/14 2:58 AM, Nathan K Houtz wrote:
Dr. Lemkul,
Thank you again - your tutorials are very helpful for me. I want to get through
your Virtual Sites tutorial but I got stuck near the beginning. Gromacs thinks
the minim.mdp file is for an earlier version but the introduction page said
i
ary. Is the file outdated, or have I
made a mistake?
Regards,
N.H.
- Original Message -
From: "Justin Lemkul"
To: gmx-us...@gromacs.org
Sent: Monday, November 10, 2014 7:40:58 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On 11/10/14 3:07 AM, Nathan K H
(examples are acetonitrile and others) and my tutorial on doing just this.
-Justin
Thanks again in advance - I really appreciate the help!
N.H.
- Original Message -
From: "Justin Lemkul"
To: gmx-us...@gromacs.org
Sent: Tuesday, November 4, 2014 7:45:39 AM
Subject: Re: [gmx-users
en it's saying the bonds are
rotating more than 30 degrees, is that the bond angle changing or does it mean
that a dihedral is changing by that much?
Thanks again in advance - I really appreciate the help!
N.H.
- Original Message -
From: "Justin Lemkul"
To: gmx-us...@g
On 11/4/14 12:45 AM, Nathan K Houtz wrote:
Thanks for your reply. However, I'm still confused. I thought that the command:
#include "oplsaa.ff/tip3p.itp"
is a call to the opls-aa force field. If this is not the correct way to include
the force field parameters, how should I do that?
That
riginal Message -
From: "Justin Lemkul"
To: gmx-us...@gromacs.org
Sent: Monday, November 3, 2014 12:44:52 PM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On 11/3/14 12:50 AM, Nathan K Houtz wrote:
> Sorry everybody, I accidentally unsubscribed from the mailing list an
On 11/3/14 12:50 AM, Nathan K Houtz wrote:
Sorry everybody, I accidentally unsubscribed from the mailing list and missed
my last response. Dr. Lemkul posted a message but I can't reply directly to it,
so here's what he said:
Your topology is constructed incorrectly, but without seeing it in
some example file and tried
to make the numbers fit appropriately under the headings. If it's not correct,
why didn't gromacs complain when I solvated it? Doesn't it read in the topology
file then as well?
I'm subscribed again so I won't miss a reply. Thanks again
On 10/26/14 10:49 PM, Nathan K Houtz wrote:
Thanks for your help. And actually my version of gromacs does not have genbox
anymore. (http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at
the bottom: GENBOX - This tool has been split to gmx solvate and gmx
insert-molecules.) But
in for all your help!
N.H.
- Original Message -
From: "Mark Abraham"
To: "Discussion list for GROMACS users"
Sent: Saturday, October 25, 2014 6:10:21 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On Sat, Oct 25, 2014 at 7:23 AM, Nathan K Houtz wrot
Hi -
genbox must work. You add the first molecule, then the second molecule
and so on. So, I suggest to run genbox for a few times and have enough
empty space available in the box. Otherwise, there is a wonderful tool
called PACKMOL.
The acid molecule looks pretty sexy. I guess it will not be ver
On Sat, Oct 25, 2014 at 7:23 AM, Nathan K Houtz wrote:
> Hello, I apologize for any ignorance but I'm quite new to gromacs and am
> confused about a few things.
>
> I want to run some simulations of a small molecule, tetrolic acid
> (CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to se
Hello, I apologize for any ignorance but I'm quite new to gromacs and am
confused about a few things.
I want to run some simulations of a small molecule, tetrolic acid
(CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to see if a united
atom approximation on the methyl group is suffic
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