[gmx-users] Mixed Solvent (H2O/CH3CN)

[Justin Lemkul]

On 3/21/15 5:51 AM, Debashis Sahu wrote:
> Dear Justin,
> Thank you for your reply. Actually, I have generated the CH3CN topology
> from the antechember. The energy minimization is completed smoothly but In
> the NVT mdrun after 11500 steps it fails. In this incomplete NVT
> trajectory, the structure of the CH3CN looks good. Still I did not get the
> actual reason for this problem. I am waiting for your suggestion to
> overcome the problem.
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

Do something easy - MD of a single CH3CN in vacuo, if that looks fine, put a 
single CH3CN in water and simulate, etc.

-Justin

> [ moleculetype ]
> ;name            nrexcl
>   ACN            3
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
> bond_type
>       1   c3     1   ACN     C    1    -0.045000     12.01000 ; qtot -0.045
>       2   hc     1   ACN     H    2     0.070700      1.00800 ; qtot 0.026
>       3   hc     1   ACN    H1    3     0.070700      1.00800 ; qtot 0.096
>       4   hc     1   ACN    H2    4     0.070700      1.00800 ; qtot 0.167
>       5   c1     1   ACN    C1    5     0.208700     12.01000 ; qtot 0.376
>       6   n1     1   ACN     N    6    -0.375800     14.01000 ; qtot 0.000
>
> [ bonds ]
> ;   ai     aj funct   r             k
>       1      2   1    1.0920e-01    2.8225e+05 ;      C - H
>       1      3   1    1.0920e-01    2.8225e+05 ;      C - H1
>       1      4   1    1.0920e-01    2.8225e+05 ;      C - H2
>       1      5   1    1.4700e-01    3.0819e+05 ;      C - C1
>       5      6   1    1.1380e-01    8.4893e+05 ;     C1 - N
>
> [ pairs ]
> ;   ai     aj    funct
>       2      6      1 ;      H - N
>       3      6      1 ;     H1 - N
>       4      6      1 ;     H2 - N
>
> [ angles ]
> ;   ai     aj     ak    funct   theta         cth
>       1      5      6      1    1.7850e+02    4.8618e+02 ;      C - C1     -
> N
>       2      1      3      1    1.0835e+02    3.2995e+02 ;      H - C      -
> H1
>       2      1      4      1    1.0835e+02    3.2995e+02 ;      H - C      -
> H2
>       2      1      5      1    1.0975e+02    4.0376e+02 ;      H - C      -
> C1
>       3      1      4      1    1.0835e+02    3.2995e+02 ;     H1 - C      -
> H2
>       3      1      5      1    1.0975e+02    4.0376e+02 ;     H1 - C      -
> C1
>       4      1      5      1    1.0975e+02    4.0376e+02 ;     H2 - C      -
> C1
>
> [ dihedrals ] ; propers
> ; treated as RBs in GROMACS to use combine multiple AMBER torsions per
> quartet
> ;    i      j      k      l   func    C0         C1         C2         C3
>        C4         C5
>       2      1      5      6      3    0.00000    0.00000    0.00000
>   0.00000    0.00000    0.00000 ;      H-     C-    C1-     N
>       3      1      5      6      3    0.00000    0.00000    0.00000
>   0.00000    0.00000    0.00000 ;     H1-     C-    C1-     N
>       4      1      5      6      3    0.00000    0.00000    0.00000
>   0.00000    0.00000    0.00000 ;     H2-     C-    C1-     N
>
>
> On Fri, Mar 20, 2015 at 5:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/19/15 8:29 AM, Debashis Sahu wrote:
>>
>>> Dear Gromacs users,
>>>                                I have faced a problem recently for the NVT
>>> simulation of a small organic receptor in acetonitrile solvent. I got the
>>> following errors even varying the box sizes as well as the number of
>>> solvent.
>>>
>>> starting mdrun 'Giant Rising Ordinary Mutants for A Clerical Setup in
>>> water'
>>> 50000 steps,    100.0 ps.
>>> step 11500, remaining runtime:   135 s          Segmentation fault (core
>>> dumped)
>>>
>>> To examine the effect of role acetonitrile, I have also used the mixed
>>> solvent box(water and acetonitrile). I have observed the similar problem.
>>> But it is interesting that when I have used simple water solvent box the
>>> simulation running smoothly. Can anyone help me to overcome this problem.
>>>
>>>
>> If every run with acetonitrile fails, you probably have a problem in the
>> acetonitrile topology.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
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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

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