[gmx-users] Re: User defined Potential Table
Rahul Godawat
godawr at rpi.edu
Tue Apr 4 09:22:27 CEST 2006
Thank you Yang,
It was really helpful, but after doing this, the mdrun asks me table.xvg and
tablep.xvg. I read about these files and I found a fix by just copying the
file table6-12.xvg from top directory as table.xvg and tablep.xvg in the
working directory seems to work. I think it is correct but I am not sure,
any comments.
Thanks once again
Rahul
-----Original Message-----
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Sent: Tuesday, April 04, 2006 2:26 AM
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Today's Topics:
1. QM/MM Compatible CPMD-3.11.1 Released! (Pradip Kumar Biswas)
2. Re: H211 in ffG53a5 (David Mathog)
3. ???? (???)
4. Building Helical Polymer (Rahul B Kasat)
5. User defined Potential Table (Rahul Godawat)
6. (no subject) (raja)
7. Re: User defined Potential Table (Yang Ye)
8. Membrane error (Kushal Seth)
9. Re: Membrane error (X.Periole)
----------------------------------------------------------------------
Message: 1
Date: Mon, 3 Apr 2006 16:54:15 -0400
From: Pradip Kumar Biswas <p.biswas at csuohio.edu>
Subject: [gmx-users] QM/MM Compatible CPMD-3.11.1 Released!
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <b47b0f9e4b9aafbb569a4fa207891cd5 at csuohio.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hello Gmxers,
This is to inform you that the CPMD code which is now
compatible to do QM/MM with Gromacs (as the driver )
is released and is available for free subject to a license
agreement with the CPMD developers.
The QM/MM modified gromacs code is available at:
http://comppsi.csuohio.edu/groups/qmmm.html
(We have posted an example of qm/mm with P450 heme
and additional examples will be uploaded soon).
and the CPMD code is available at: http://www.cpmd.org
Cheers,
PB.
------------------------------
Message: 2
Date: Mon, 03 Apr 2006 14:26:41 -0700
From: "David Mathog" <mathog at caltech.edu>
Subject: Re: [gmx-users] H211 in ffG53a5
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <E1FQWZN-0007ni-00 at mendel.bio.caltech.edu>
Content-Type: text/plain; charset=iso-8859-1
Ken Rotondi wrote:
> I've had this in AMBER for some time. I need to use a
> UAFF.
ok
> >
> > There is no H211 in either the .hdb or .pdb file.
My first guess would be that even though you say it's not
in there, it actually is. Perhaps it's in lower case and you
used a case sensitive search? Try
grep -i h211 *.hdb *.pdb
and see if it turns up.
-ignh might also be helpful (doubt it though). If all else fails
backtrace through the code from the location of the error message
until you find where that atom is coming from.
Regards,
David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
------------------------------
Message: 3
Date: Tue, 4 Apr 2006 06:36:28 +0900 (KST)
From: ??? <praise at kaist.ac.kr>
Subject: [gmx-users] ????
To: gmx-users at gromacs.org
Message-ID: <12192596.2514791144100188696.JavaMail.kebi at webmail>
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Message: 4
Date: Mon, 3 Apr 2006 20:01:28 -0400 (EDT)
From: Rahul B Kasat <rkasat at ecn.purdue.edu>
Subject: [gmx-users] Building Helical Polymer
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <Pine.GSO.4.61.0604031957050.13804 at atom.ecn.purdue.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Hi Everyone:
I am a new user of GROMACS.
I am interested in building a new helical polymer (6 monomers per helical
turn) in gromacs with periodic boundary conditions.
Can someone please guide me through this?
Thanks,
- Rahul
****************************************************************************
*********
Rahul Kasat
Purdue University,
West Lafayette, IN 47907
****************************************************************************
*********
------------------------------
Message: 5
Date: Mon, 3 Apr 2006 19:39:20 -0400
From: "Rahul Godawat" <godawr at rpi.edu>
Subject: [gmx-users] User defined Potential Table
To: <gmx-users at gromacs.org>
Message-ID: <000001c65777$da664ce0$5ee47180 at Rahul>
Content-Type: text/plain; charset="us-ascii"
Hi Berk,
Groamcs user forum has really been extremely useful so far to work with
gromacs. I want to apply a user defined potential for selected energy
groups. Its hard to interpret the information on the gromacs webpage and
even going through mailing list archives did not answer many questions I
have.
All of my energy groups would interact with normal LJ and use PME for
coulombtype (if they have charges) except for 3-4 combinations I want to use
WCA potential which has a well defined functional form. How would you
suggest going about it.
Thank you very much
Rahul
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Message: 6
Date: Mon, 03 Apr 2006 21:19:05 -0700
From: "raja" <raja_28 at fastmail.us>
Subject: [gmx-users] (no subject)
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID: <1144124345.23754.258244479 at webmail.messagingengine.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear gmxions,
How to set the coordination bond between Fe(II) in activesite and three
atoms of protein residues in gromacs MD run ?
With thanks !
B.Nataraj
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - Send your email first class
------------------------------
Message: 7
Date: Tue, 04 Apr 2006 13:02:50 +0800
From: Yang Ye <leafyoung81-group at yahoo.com>
Subject: Re: [gmx-users] User defined Potential Table
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4431FDFA.5060407 at yahoo.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi, Rahul
You need an index file for this purpose. Use make_ndx to generate an
index file which contains one group including all atoms. Name this group
as system. Then, you may take down the atom number for those 3-4
combinations and put them as one group in the index file, while removing
them from the [ system ]. Name this new group as [ WCA ].
In your mdp file, put following lines
energygrps = system WCA
table-extension = 0
energygrp_table = WCA WCA
Then you need to generate the parameter file, name them as
table_WCA_WCA.xvg. A complete list shall include all combination of the
group, WCA v.s. system, system v.s. system. But they shall follow the
standard way, so you may just skip the definition.
For the meaning of the columns inside the table, check manual as well as
check table#-##.xvg inside the top directory.
This is not a complete tutorial so you may encounter some error
messages. Just follow the instructions given, you shall be able to do it.
Yang Ye
Rahul Godawat wrote:
>
> Hi Berk,
>
>
>
> Groamcs user forum has really been extremely useful so far to work
> with gromacs. I want to apply a user defined potential for selected
> energy groups. Its hard to interpret the information on the gromacs
> webpage and even going through mailing list archives did not answer
> many questions I have.
>
>
>
> All of my energy groups would interact with normal LJ and use PME for
> coulombtype (if they have charges) except for 3-4 combinations I want
> to use WCA potential which has a well defined functional form. How
> would you suggest going about it.
>
>
>
> Thank you very much
>
>
>
> Rahul
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------
Message: 8
Date: Tue, 4 Apr 2006 00:17:25 -0500
From: "Kushal Seth" <kushalseth at gmail.com>
Subject: [gmx-users] Membrane error
To: gmx-users at gromacs.org
Message-ID:
<85d54ee10604032217v78326c14tc29989224c8c8b7f at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
HI all !
> I am gettting this error while doing my simulation... for the bilayers
>
>
>
> Back Off! I just backed up emout-nowater.mdp to ./#emout-nowater.mdp.1#
> checking input for internal consistency...
> ...ling /usr/bin/cpp
> : No such file or directory
> cpp exit code: 32512
> -I/usr/local/gromacs/share/gromacs/top mytop-nowater1.top > gromppdriwHo'
> ' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: grompp.c, line: 427
>
> Fatal error:
> number of coordinates in coordinate file (binaryCR-Ochol-box-largeZ.pdb,
> 10280)
> does not match topology (mytop-nowater1.top, 0)
>
> I would appreciate if anyone can help me out with this.
> Thanks
> Kris
>
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Message: 9
Date: Tue, 04 Apr 2006 08:22:14 +0200
From: "X.Periole" <X.Periole at rug.nl>
Subject: Re: [gmx-users] Membrane error
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <web-18505295 at mail3.rug.nl>
Content-Type: text/plain; charset="ISO-8859-1"; format="flowed"
On Tue, 4 Apr 2006 00:17:25 -0500
"Kushal Seth" <kushalseth at gmail.com> wrote:
> HI all !
>> I am gettting this error while doing my simulation...
>>for the bilayers
>>
>>
>>
>> Back Off! I just backed up emout-nowater.mdp to
>>./#emout-nowater.mdp.1#
>> checking input for internal consistency...
>> ...ling /usr/bin/cpp
>> : No such file or directory
>> cpp exit code: 32512
>> -I/usr/local/gromacs/share/gromacs/top
>> mytop-nowater1.top > gromppdriwHo'
>> ' command is defined in the .mdp file
>> processing topology...
>> processing coordinates...
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3
>> Source code file: grompp.c, line: 427
>>
>> Fatal error:
>> number of coordinates in coordinate file
>>(binaryCR-Ochol-box-largeZ.pdb,
>> 10280)
>> does not match topology (mytop-nowater1.top,
>>0)
>>
there is definitely a problem in the definition of your
system in the mytop-nowater1.top ... the systm does not
see
any atom in there.
XAvier
------------------------------
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