[gmx-users] how to know solvent molecule number
cbb.chintan at gmail.com
Mon Apr 10 16:15:01 CEST 2017
As You advised, I tried grep -c option
My solvent file - ethanolamine.gro
1DRG OAC 1 -0.083 0.327 0.043
1DRG HAE 2 -0.146 0.373 -0.019
1DRG CAB 3 -0.074 0.188 0.009
1DRG HAC 4 -0.172 0.143 0.025
1DRG HAD 5 -0.037 0.178 -0.093
1DRG CAA 6 0.022 0.117 0.105
1DRG HAA 7 0.026 0.011 0.079
1DRG HAB 8 -0.015 0.136 0.206
1DRG NAD 9 0.158 0.174 0.097
1DRG HAG 10 0.193 0.162 0.004
1DRG HAH 11 0.217 0.125 0.161
1DRG HAF 12 0.155 0.271 0.120
0.53926 0.53926 0.53926
So, I tried OAC as unique atom to count the number of ethanolamine (solvent
molecule) in my box.
*lab1 at lab1-desktop:~/Desktop/md2$ grep -c OAC 1AKI_solv.gro10067*
As i understand that my box is fully filled with 10067 ethanolamine
molecules which indicate this will be stimulation in 100% ethanolamine (if
I do further). If I want to do stimulation with 20% ethanolamine - 80%
water. Then, number of ethanolmine should come around 2013 molecule
(OAC=2013) in 1AKI_solv.gro file.
Is it correct?
On Wed, Apr 5, 2017 at 7:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 4/5/17 9:12 AM, Chintan Bhagat wrote:
>> I want to do stimulation of my protein in solvent, ethanolamine (different
>> I have made box of 1 nm and then using command
>> "gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
>> As per my knowledge, i solvated my protein in ethanolamine.
>> Now I want to know the number of ethanolamine molecule present in box.
>> I looked in to *.top* file but no information is availble in the file
>> (As per intruction, program is only hard-coded to update the topology in
>> the case of water).
>> I found increase in number of molecules from 7200 to 128004 in
>> /home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
>> respectively. It means something is inserted in box (must be
>> ethanolamine!!!!!-my guess)
>> How can i know number of ethanolamine molecules?
> Use grep -c with a unique atom name to count the number of any given
> molecule in the system.
>> for reference please find attched files.
> The mailing list does not accept attachments.
> 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
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