[gmx-users] Re: Re: Re: Electrostatics of Rigid Water

Justin M. Shorb shorb at wisc.edu
Mon Aug 7 22:03:55 CEST 2006

Greetings all!

Thank you for your suggestions. I have figured out my problem with  
getting different electrostatic forces from the same input file with  
regards to flexible vs. rigid water. I wanted to post the results here  
in case anyone in the future looks into the archives.

The initial setup for settle is called before the MD loop begins, and  
actually moves all the atoms a slight amount from the initial input  
file. This small discrepancy accounted for my previous disagreement  
between rigid and flexible water. Thus it was not the kernel that had  
changed, but the positions of the atoms.


> Date: Thu, 03 Aug 2006 20:22:32 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Electrostatics of Rigid Water
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <44D23EE8.2090709 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Justin M. Shorb wrote:
>> Greetings!
>> I am running a modified version of Gromacs 3.3 that calls the
>> do_nonbonded subroutine twice, in order to calculate specific
>> interactions. Unfortunately for my purposes, the settle restraints
>> (which I would assume to be a 'bonded' interaction) seem to be called
>> within the nb_kernel. Is there a flag that I can reset within gromacs  
>> to
>> temporarily turn off the subroutine that runs the settle potential
>> calculation? I have been searching, but cannot seem to find where this
>> is even called. If I run a single step MD run without settle (define =
>> -DFLEXIBLE, with SPC/E force constants set to zero) then I obtain the
>> correct coulombic interaction potential, otherwise there is a  
>> discrepancy.
>> Currently, the non_bonded subroutine is called using the following:
>>   if (fcoul) /* added */
>>       do_nonbonded(fplog,cr,fr,x,fcoul,md, /* added */
>>          grps->estat.ee[egCOULSR], /* added */
>>          grps->estat.ee[egCOULSR],box_size,nrnb, /* added */
>>          lambda,&dvdlambda,FALSE,-1,-1,bDoForces); /* added */
>> Also, I am surprised that by substituting the COULSR table where the  
>> LJ
>> table is usually passed allows for the complete neglect of LJ without
>> the (expected?) doubling of the coulombic force, although the  
>> coulombic
>> potential is doubled. I believe I read in the code that there is a  
>> check
>> in the inner loop to make sure that no forces are redundantly
>> calculated, but any further clarification would be appreciated (as  
>> this
>> was discovered empirically).
> the settle algorithm is a constraint algorithm and is called from the
> update routine.
>> Thanks in advance!
>> Justin
>> _________________________________________________________________
>> Justin M. Shorb            Phone: (608) 262-0483
>> Skinner Group                shorb at wisc.edu
>> University of Wisconsin-Madison,  Department of Chemistry
>> 1101 University Ave., Madison, WI, 53706
>> _______________________________________________
>> 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
> --  
> David.
> _______________________________________________________________________ 
> _
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> +
Justin M. Shorb			Phone: (608) 262-0483
Skinner Group				shorb at wisc.edu
University of Wisconsin-Madison,  Department of Chemistry
1101 University Ave., Madison, WI, 53706
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 3968 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060807/464e9406/attachment.bin>

More information about the gromacs.org_gmx-users mailing list