Re: [gmx-users] New ion parameters and OPLS-AA

[eladp]

Hi Reza,



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Message: 4
Date: Tue, 15 Dec 2009 14:03:36 -0800 (PST)
From: Reza Salari resa...@yahoo.com
Subject: Re: [gmx-users] New ion parameters and OPLS-AA
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 858209.12986...@web35303.mail.mud.yahoo.com
Content-Type: text/plain; charset=us-ascii

Thanks for your response.

While I will try that (although it seems it needs quite amount of  
scripting), I remember in the past some people in the mailing list  
mentioned problems while using nonbond_params directvie with OPLS-AA  
and in response it was generally suggested to avoid doing this kind  
of mixing. Like Dr Abraham suggestion here:


http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html

Have you tried this kind of mixing for OPLS successfully, without  
being overridden by the default rules?


I have successfully done so.
My topology looks like this:


#include ffoplsaa.itp

[ nonbond_params ]
opls_272   opls_412  1 0.277  1.2857

#include frm.itp


; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif

.
.
.


Of course there should be a line for every possible pair interaction.
It is important to put the [ nonbond_params ] after the include to  
ffoplsaa.itp




The main thing that I am still unsure about is how the previously  
mentioned paper converted the sigma values for different combination  
rules. It seems that there must be a relatively direct way to do  
this without going through the re-parametrization process.


Regards,
Reza Salari




From: Andrew Paluch apal...@nd.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, December 15, 2009 4:34:18 PM
Subject: Re: [gmx-users] New ion parameters and OPLS-AA

Read the manual.  You can explicitly declare all of your cross terms  
rather than using the same mixing rule for all terms.  You can  
easily write a script to modify your input files accordingly,


Andrew


On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote:

Hi All,


Recently there has been a new set of ion parameters published by  
Joung and Chetham and I am interested in running some test runs  
using these parameters. These set of parameters are based on using  
LB rule (arithmetic mean) for sigmas.


However I am using OPLS-AA ff so I am using the combination rule 3  
(geometric mean of corresponding A and B values). My question is  
that can I use the exact sigma values from Cheatham for my  
simulations? I'm almost positive that I have to change these sigma  
values to be consistent with the combination rule that I am using.  
In fact there is a paper by Horinek et al that has a nice table of  
different ionic sigma and epsilon values from different parameter  
sets (Aqvist, Jensen, Cheatham,..). The article is

here:
http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes

In that table, they have mentioned two sigmas; a usual sigma (which  
is used with rule 2) and a sigma prime (which can be used with rule  
3). However it seems sort of unclear to me how they got these value  
since in some references that they've mentioned I could find either  
sigma or sigma prime, not both. So I am guessing there must be some  
way to convert these two sigmas to each other.


So does anyone know if there is such way? Does GROMACS internally  
treats sigmas as sigma prime for OPLS-AA? I looked at the manual  
and also searched the mailing list to find an explanation but  
without luck. I really appreciate any help on

clarifying this.

Regards,
Reza Salari

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[gmx-users] g_mindist after trjconv -fit give different results

[eladp]

Hi Tsjerk,
thanks for the reply.

Will the MSD of the molecule also be affected by the fitting.
I'm trying to calculate the relative diffusion coefficient of an ion  
near a protein. For this I thought to first fix the system according  
to the protein and then calculate the msd of the ion.
I noticed in the g_msd code that periodicity is taken into account (as  
expected). However, in g_msd the interest of the periodicity handling  
regards regards the atom position relative to itself in previous  
frames. Will this relative movement (of the atom in relation to itself  
in the previous frame) be kept after doing trjconv -fit.


Thanks.



Hi Elad,

This has been mentioned several times before, in a different context.
But fitting only affects coordinates, and not the PBC. So after
fitting the coordinates and the PBC don't match any more and any
analysis requiring PBC, such as calculating minimal distances, will
give garbled results. Always do such things on untransformed
trajectories.

Cheers,

Tsjerk

On Fri, Dec 4, 2009 at 7:43 PM,  el...@post.tau.ac.il wrote:

Hi all,

I have a system of protein+water+ions.
I measured the minimum distance between one of the ions to the protein.

Afterwards I fitted the trajectory using g_trjconv -fit rot+trans

Did the same mindist again and the graphs are not always identical.

Any suggestions?

I use gromacs 4.0.5 with an octahedron box.
same problem happens when I do trjconv -fit rot but does not happen when
-fit trans.

In VMD I do see a difference in the position of the ion relative to the
protein.

Thanks.
Elad P.





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[gmx-users] A fix to eigio.c ?

[eladp]

make_edi crashes on 3.3.3 (but not on 3.3.1).

I think the problem is in eigio.c where the following lines were added  
after 3.3.1:


  eignr=NULL;
  eigval=NULL;
  eigvec=NULL;

I guess it should be:

  *eignr=NULL;
  *eigval=NULL;
  *eigvec=NULL;

Elad P.

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[gmx-users] Re: gmx-users Digest, Vol 50, Issue 97

[eladp]

Try installing development version: openmotif-devel



Hi

I want to use grace 5.1.9 (normally xmvgr). each time i do installation
using  ./configure, it prompts motif not found .

So i tried to find free softare openmotif (it can do the same work as
motif). Having successfully installed openmotif , the grace installation ,
however, still tells me motif not found .
Gromacs 's web page proposes lesstif can also do as motif , so i downloaded
lesstif and installed it succefully , but grace prompted modtif not found
once again.
BTW: my OS is Fedora core 8

Can anyone give a good idear of installing grace..




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