[gmx-users] Different number of molecules in simulation box.

[Justin Lemkul]

On 5/3/17 8:04 AM, B Prakash wrote:
> On Wed, May 3, 2017 at 5:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> The number inserted depend on clashes with the input coordinates, so if you
>> change those, don't be surprised if the output changes :-)
>>
>
> Hi Mark,
> surprisingly, there were no changes in neither the pdb file nor the input
> commands. However genbox accomodated 13 more methanol molecules in the same
> space. The only reason for it I could imagine is minor changes in protein
> orientation.
>

If there are "minor changes in protein orientation" then you cannot say there 
are no changes in the PDB file.  If the coordinates are in any way different, 
then the overlap with the solvent will be different and you will get a different 
outcome, as Mark has said.  Do a diff on the input coordinate files to make sure 
you're doing what you think you are doing.

-Justin

>>
>> Mark
>>
>> On Wed, 3 May 2017 13:29 B Prakash <4gromacs at gmail.com> wrote:
>>
>>> On Wed, May 3, 2017 at 3:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> On Wed, May 3, 2017 at 11:24 AM B Prakash <4gromacs at gmail.com> wrote:
>>>>
>>>>> Dear all,
>>>>> am trying to do a simulation of a protein in methanol. Am using
>> gromacs
>>>>> 4.6.1.
>>>>
>>>>
>>>> Do yourself a favour and for new work, install a version that isn't
>> four
>>>> years old, has extra bugs for free, and is unsupported ;-)
>>>>
>>>
>>> Dear Mark,
>>> thank you. I will do so. However, I was curious about the difference in
>> the
>>> number of methanol molecules added when all other parameters are same.
>>>
>>>>
>>>> Am using the methanol box supplied in gromacs. In some of the
>>>>> simulations, the box took nearly 10K (10040) methanol molecules. But
>> in
>>>>> others the number varied a little (10053). In editconf command, I
>> tried
>>>> to
>>>>> center the protein in the simulation box. Is the variation in
>> methanol
>>>>> molecules due to minor changes in orientation of protein by editconf
>>> and
>>>>> genbox. Please correct.
>>>>>
>>>>
>>>> Yes. There's an option to choose the maximum number of molecules added,
>>> if
>>>> you want a little more control.
>>>>
>>>> Mark
>>>>
>>>>
>>>>> Regards,
>>>>> Prakash.
>>>>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================