[gmx-users] No cut-off

Erik Marklund erikm at xray.bmc.uu.se
Thu Mar 24 09:34:26 CET 2011

Mark Abraham skrev 2011-03-24 06.52:
> On 24/03/2011 4:38 PM, Swarnendu Tripathi wrote:
>> Hi all,
>> Thank you for the reply. The answer I got for the second question 
>> about table-extension, I understand and agree with that.
>> Regarding my first question I asked, I did not get any error with 
>> grompp even when I tried rlist=rvdw=2.0 and rcoulomb=0. For this I 
>> used the no cut-off conditions which I have mentioned below in my 
>> previous e-mail. I am using Gromacs-4.0.7.  Any further suggestions 
>> or comments will be very helpful.
> VDW interactions normally become insignificant much faster than 
> Coulomb interactions, so treating all Coulomb interactions and only 
> some VDW interactions is logical. However, performing the search for 
> neighbours takes time, and given that you are computing the distances 
> already for their Coulomb interaction, it is probably cheaper just to 
> compute all the VDW interactions, i.e. rlist=rvdw=0. This might be 
> different if you had a lot of atoms that had zero partial charge.
> Mark
In addition, depending on your system, the collective long-range 
attraction from VdW interactions may not be insignificant. And since 
you're simulating in vacuo, I guess you have an inhomogeneous system, 
and dispersion corrdection may not be adequate. That's further reason to 
have infinite VdW cut-offs too. And, as mark mentioned, the distances 
are calculated anyway, so computing VdW will not add that much to your 
simulation time.

>> On Thu, Mar 24, 2011 at 12:17 AM, Mark Abraham 
>> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>     On 24/03/2011 1:34 PM, Itamar Kass wrote:
>>         Hi Swarnendu,
>>         grompp will return errer unless rlist=rcoulomb=rvdw=0, so you
>>         should stick to it.
>>         Cheers,
>>         Itamar
>>         On 24/03/11 1:13 PM, Swarnendu Tripathi wrote:
>>             Hello everybody,
>>             I want to use the no cut-off option in gromacs for the
>>             electrostatic interactions. In manual it says for this I
>>             need to define: pbc=no; nstlist=0; ns-type=simple and
>>             rlist=rcoulomb=rvdw=0 in the .mdp file.
>>             My questions are:
>>             1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a
>>             problem? Do you always recommend to use
>>             rlist=rcoulomb=rvdw=0 for no cut-off option?
>>             2. How  should I choose the table-extension parameter
>>             now? Before, with pbc=xyz (with cut-off) I used
>>             table-extension=rvdw+1/2*length of the longest diagonal
>>             of the box (approximately). I am also using a tabulated
>>             potential.
>>     Since there is effectively no box once pbc=no, your tables need
>>     only be as long as the longest possible interaction, plus some
>>     margin for when the structure rearranges.
>>     Mark
>>     -- 
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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/

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