[gmx-users] SImulation with urea

[bharat gupta]

Thanks Justin .. problem solved...


On Wed, Mar 5, 2014 at 8:14 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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> On 3/4/14, 6:10 PM, bharat gupta wrote:
>
>> Hi,
>>
>> I have some small doubt regarding using urea in simulation. Actually, I
>> calculated the the number of urea molecules for a particular concentration
>> in the box. For eg., the same box if filled with water occupies 43614
>> molecules of water and if I need to fill molecules of urea for 1M
>> concentration, the values comes around 875. I added, those urea molecules
>> using -ci and -nmol flags in genbox command. How to add the water now,
>> i.e.
>> the remaining 42379 water molecules. When I use genbox to add water it
>> replaces those Urea molecules completely and add 43614 molecules. I even
>> tried adding water and urea simultaneously, in that case the urea
>> molecules
>> are added as per the given number, but the number of water molecules added
>> are lesser than 42379, which should be 43614. What am I going wrong ??
>>
>> For adding water and urea simultaneously, I used the following command:
>> genbox -cp newbox,gro -cs spc216.gro -ci Urea.gro -nmol 875 -o solv.gro -p
>> topol.top
>>
>>
> Doing these two processes simultaneously is asking for trouble and will
> probably fail.  I don't understand the statement above about genbox
> removing urea - the program shouldn't do that (genion replaces molecules,
> genbox adds them).  Do the additions in two steps:
>
> 1. Add urea with -ci -nmol
> 2. Simply fill the rest of the box like would would anything else with
> genbox -cs spc216.gro -cp system_with_urea_already_added.gro
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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