[gmx-users] Reg: Adding multiple molecules
kmvinoth at gmail.com
Mon Sep 27 13:34:10 CEST 2010
Thank you for your suggestion.
On Mon, Sep 27, 2010 at 4:52 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> vinothkumar mohanakrishnan wrote:
>> Hi justin
>> if genbox is not able to find sufficient space then why should one
>> calculate number density for the given box dimension?.similarly the the
> Just because you can calculate a certain number density does not
> necessarily mean that the algorithm genbox is using can produce such a
> configuration. It inserts molecules randomly, so you may be able to find a
> magical value of -seed for which this will work. The simpler approach is
> what I suggested earlier.
> number of molecules are not getting updated in the molecules section of
>> the topology file when inserting multiple molecules using the genbox
>> command. everytime i need to update it manually.is <http://manually.is>
>> there a way to update it automatically?
> The topology will only be updated automatically when adding water.
> Otherwise, you have to do it yourself.
>> On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>> vinothkumar mohanakrishnan wrote:
>> Hi all
>> I have a diffculty in adding multiple molecules of hexane to my
>> box. my box size is 4.72*2.36*2.36 (nm) according to my number
>> density calculations the box should fit 124 molecules of hexane
>> whereas it adds only 76 molecules to the box below is my
>> command. i had evev tried with -try command but without sucess.
>> genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o
>> hexane-multi.gro -nmol 124 -seed 1268
>> If you're not getting all the molecules you want, then genbox is
>> unable to find sufficient space for them. Try a larger box, then
>> -- ========================================
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> 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
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