[gmx-users] Re: User defined Potential Table

[Yang Ye]

Hi, Rahul

Yes. I think that shall be fine. They shall be there for system vs.
system, and WCA vs. system, which we did not specified in the mdp. I
recommend you to check your energies with previous set-up. You need to
check whether

*    new set-up's energy = original energy - internal potential of 3-4
groups + WCA potential of 3-4 groups.*

P.S. Use nstep=1 to get the energy.

Yang Ye


Rahul Godawat wrote:
> 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-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of gmx-users-request at gromacs.org
> Sent: Tuesday, April 04, 2006 2:26 AM
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 24, Issue 8
>
> Send gmx-users mailing list submissions to
> 	gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> 	gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> 	gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> 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>
> Content-Type: text/plain; charset="us-ascii"
>
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20060404/1ac551ac/att
> achment-0001.html
>
> ------------------------------
>
> 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
>
>  
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20060403/91e3006f/att
> achment-0001.html
>
> ------------------------------
>
> 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
>
>