[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT

[vivek sinha]

Hey Justin,
I will tell you the steps that I took for the simulation from the beginning.
1. Generated a tube online
http://turin.nss.udel.edu/research/tubegenonline.html
2. Attched Hydrogen to it using pymol and converted to .gro and then .top
file
3. Solvated using genbox -cp cnt_sl.gro -cs spc216.gro -o cnt_solvated.gro
-p topol.top
4. Remove atoms from center using c++ script which does not numbers the
atoms again. My 12663 atoms changed to 12183 after this.
5. Energy minimisation: grompp -f minim.mdp -c ___.gro -p ___.top -o em.tpr
mdrun -v -deffnm em

The next step about equibilating is giving a segmentation fault.
The minim.mdp is
-----------------------------------
; minim.mdp - used as input into grompp to generate em.tpr
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps        = 50000          ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist            = 1            ; Frequency to update the neighbor list
and long range forces
cutoff-scheme   = Verlet
ns_type            = grid        ; Method to determine neighbor list
(simple, grid)
coulombtype        = PME        ; Treatment of long range electrostatic
interactions
rcoulomb        = 0.9        ; Short-range electrostatic cut-off
rvdw            = 0.9        ; Short-range Van der Waals cut-off
pbc                = xyz         ; Periodic Boundary Conditions (yes/no)
-----------------------------------
And I have already sent you the nvt.mdp settings that I am using.

Please help me in completing my simulation.

Thanking You,
Vivek Sinha






On Wed, Jul 16, 2014 at 1:25 PM, vivek sinha <viveksinha20002 at gmail.com>
wrote:

> But mdrun doesnt update these information/new numbering in the topology
> file. I mean the topology fie would be saying that there is a bond between
> 101 and 105 and if I removed those atoms, the mdrun would have assignmed
> 101 and 105 to some other atom and hence it can create problems.
>
> Is this possible?
>
>
> On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/15/14, 2:19 PM, vivek sinha wrote:
>>
>>> Hey Justin,
>>> I think I understood the problem. When I removed the solvent from inside
>>> CNT, I kept the numbering of atoms just like before without actually
>>> making
>>> a new strictly increasing order numbering. But now when I see that after
>>> the energy minimization the new pdb file got arranged strictly by
>>> increasing order.
>>>
>>> As an example. After deleting atoms inside the CNT, my .gro file did not
>>> had the atom no 6292, but after energy minimisation the em.gro file
>>> contains the atom no 6292. This must have created a renumbering of the
>>> atoms. Not good I suppose.
>>> Please suggest what to do?
>>>
>>> The concern is that whether to renumber the molecules after removing the
>>> water from inside the CNT or not?
>>>
>>>
>> The numbering in the input coordinate file is irrelevant.  The output of
>> mdrun is always numbered consecutively from 1.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>