[gmx-users] Re:Re: tpbconv -zeroq results all coulombic energies to zero

[BIN ZHANG]

Dear David:

Thanks a lot for your reply. You are absolutely right! All the charges  
in the tpr file is zero now.

This does not make much sense to me though, as the group I selected  
with "tpbconv" does not include all the atoms. I also tried to use  
other groups such as POPC or Protein and none of them give me sensible  
results (the charges are not all set to zero). Is this supposed to be  
a bug?

Thanks,
Bin


>
> On 2010-12-03 08.45, BIN ZHANG wrote:
>> Hi, all:
>>
>> I was trying to use "tpbconv" to modify the tpr file with the  
>> command:
>> tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr
>>
>> It basically sets the charge of one group to zero. However, when I
>> perform mdrun -rerun, all the coulombic energies are zeros, i.e.,
>> Coulomb-(SR), Coul.-recip. This really does not make sense since I  
>> still
>> have atoms in other groups that are charged. I was using  
>> gromacs4.0.7.
>>
> Please check using gmxdump that there still are charged groups left  
> in your tpr file.
>
>> Has anyone seen this before? What exactly is the correct way to  
>> zeroize
>> the charge for a group of atoms?
>>
>> Thanks,
>> Bin
>>
>
>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>
>
>
>
> From: Olga Ivchenko <olga.ivchenko at gmail.com>
> Date: December 3, 2010 12:31:50 AM PST
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] proton proton transfer
> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>
> Hi Erik,
> I think also I can try proton-proton transfer with gromacs later  
> when it will be implemented.
>
> best,
> Olga
>
> 2010/12/2 Erik Marklund <erikm at xray.bmc.uu.se>
> Olga Ivchenko skrev 2010-12-02 13.30:
>
> Dear gromacs users,
>
> I want to simulate proton transfer between water and another small  
> molecule in gromacs. In the end I should have the velosity of proton  
> proton exchange. Please can you advice me which method is better to  
> use for this in gromacs.
> I read about umbrella sampling, but may be there is other techniques?
>
> Yours sincerely,
> Olga
> I am working on a protocol to include proton transfer in classical  
> gromacs simulations. Unfortunately it will note be ready for at  
> least a month, so if you're in a hurry you'll have to do it with  
> e.g. QM/MM.
>
> Erik
>
> -- 
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
>  before posting!
> 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/Support/Mailing_Lists
>
>
>
> -- 
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
>  before posting!

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101203/a4f4e319/attachment.html>