[gmx-users] CNT md simulation & unusual minimized structure

[Justin Lemkul]

On 7/19/18 7:08 AM, Atila Petrosian wrote:
> Dear gromacs users,
>
> I am doing md simulation of cnt + drug (lig) + water molecules.
>
>
>
> I get lig.gro and lig.itp files using antechamber module and amb2gmx script.
>
>
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> I used cnt force field parameters from paper
> (*https://pubs.acs.org/doi/abs/10.1021/jp011344u
> <https://pubs.acs.org/doi/abs/10.1021/jp011344u>*)
>
>
>
> I get pdb file of cnt from nanotube modeller: (18,0), (Length = 34.468 Angstrom)
>
>
>
> gmx_mpi editconf -f cnt.pdb -o cnt.gro -c -box 8 8 3.4468
>
>
>
> gmx_mpi x2top -f cnt.gro -o cnt.top -ff cnt -name CNT -pbc -noparam
>
>
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> I merged gro files and itp and top files without problem.
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> gmx_mpi grompp -f em_vac.mdp -c complex.gro -p topol.top -o em_vac.tpr
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> gmx_mpi mdrun -v -deffnm em_vac -nb gpu >& em_vac.job &
>
>
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> gro file after energy minimization is unusual.
>
>
>
> https://1drv.ms/u/s!AveJH4Y30cH0sQnyV-5RoaqhaeFJ

It looks like your box fits the CNT exactly and does not leave enough 
space for bonds between images, so you get distortion at the "ends" of 
the central image.

-Justin

>
>
>
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> lig.itp, topol.top and cnt.ff is as follows, respectively:
>
>
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> https://1drv.ms/u/s!AveJH4Y30cH0sHioMbu0GT2BDATg
>
>
>
> https://1drv.ms/u/s!AveJH4Y30cH0sHrSTs-0f0kK-mE5
>
>
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> https://1drv.ms/f/s!AveJH4Y30cH0rEU08meMh0EEfQde
>
>
>
>
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> Please guide me to resolve this problem.
>
>
> Best,
>
> Atila

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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