Thanks for the suggestion Chris. Had a quick look and can't see easily how to
do this, but I think I am at a point now where it is not an issue and don't
have to actually do this.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, M
f Michael Shirts
> Sent: Thursday, 31 October 2013 1:52 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] RE: Gibbs Energy Calculation and charges
>
> I likely won't have much time to look at it tonight, but you can see
> exactly what the option is doing to t
I likely won't have much time to look at it tonight, but you can see
exactly what the option is doing to the topology. run gmxdump on the
tpr. All of the stuff that couple-intramol does is in grompp, so the
results will show up in the detailed listings of the interactions, and
which ones have whi
Michael, thanks for taking the time to comment and have a look.
The real issue I am having is a bit deeper into the topic than that, my last
reply was just an observation on something else. Will summarise what I have
been doing etc.
I have a molecule that are calculating the Gibbs energy of hy
Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.war...@monash.edu
>> +61 3 9903 9304
>> -----
>> When the only tool you own is a hammer, every problem begins to
>> rese
.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Dallas Warren
> Sent: Tuesday, 22 October 2013 2:49 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] RE: Gibbs Energy Calculation and charges
>
&
to resemble a
nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Dallas Warren
> Sent: Thursday, 17 October 2013 3:32 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] RE: Gibbs Energy Ca
Chris,
Thank you, that appears to be the issue then.
Running them again now with couple-intramol = yes
Will report back once that is completed with the results.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
38
Chris,
You are correct in the first part of your statement, part that isn't correct is
I expect for the same charge on the atom I expect it to give the same dH/dl
value.
For example, for the OE atom that I provided the graphs for (
http://ozreef.org/stuff/octanol.gif and http://ozreef.org/stuf
Here is the molecule in octanol
http://ozreef.org/stuff/octanol.gif
And here in water
http://ozreef.org/stuff/water.gif
Just realised, it is actually quite different in water, consistently.
So the only difference between the two simulations is the charges on the
molecule have been multiplied by
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