[gmx-users] destruction of the structure of a molecule in water after energy minimization
Justin Lemkul
jalemkul at vt.edu
Wed May 31 02:11:09 CEST 2017
On 5/30/17 2:27 AM, Saeed Nasiri wrote:
> Dear all
>
> I created the topology and itp files for a molecule manually (the
> parameters are not exist in the usual force fields) and build a box of a
> molecule and 857 water molecules. The structure of the molecule in water
> box is OK. Then the energy minimization step was done by the following
> files. After the successful termination, the structure of the molecule has
> been destroyed and the atoms of the molecule are spread in the box. In the
> following the employed files and the structure of the molecule (in gro
> format) before and after minimization (without water molecule) are
> presented.
> Any help will highly appreciated.
>
The problem likely lies in the topology of this molecule. If it falls apart in
vacuo, that's the issue and you need to revisit your parametrization.
-Justin
> ####################### before minimization ###############################
> 1BM CW 1 1.222 1.373 1.397
> 1BM CW 2 1.349 1.331 1.419
> 1BM CR 3 1.308 1.498 1.557
> 1BM HCW 4 1.148 1.339 1.327
> 1BM HCW 5 1.408 1.254 1.371
> 1BM HCR 6 1.318 1.570 1.636
> 1BM NA 7 1.196 1.475 1.486
> 1BM NA 8 1.400 1.408 1.521
> 1BM C1 9 1.540 1.411 1.566
> 1BM H1 10 1.571 1.308 1.584
> 1BM H1 11 1.541 1.464 1.662
> 1BM C2 12 1.631 1.482 1.466
> 1BM HC 13 1.588 1.580 1.446
> 1BM HC 14 1.630 1.426 1.372
> 1BM CS 15 1.774 1.494 1.518
> 1BM HC 16 1.814 1.395 1.542
> 1BM HC 17 1.774 1.551 1.611
> 1BM CT 18 1.867 1.563 1.418
> 1BM HC 19 1.831 1.663 1.394
> 1BM HC 20 1.969 1.572 1.458
> 1BM HC 21 1.873 1.507 1.324
> 1BM C1 22 1.082 1.566 1.484
> 1BM H1 23 1.032 1.567 1.581
> 1BM H1 24 1.011 1.532 1.409
> 1BM H1 25 1.121 1.665 1.461
> 2Cl Cl 26 2.283 1.962 0.221
>
> #################### after minimization ###################################
> 1BM CW 1 1.030 1.807 0.330
> 1BM CW 2 1.253 0.613 1.483
> 1BM CR 3 0.962 1.561 1.355
> 1BM HCW 4 0.754 0.906 0.667
> 1BM HCW 5 1.875 0.398 0.729
> 1BM HCR 6 0.982 2.417 2.358
> 1BM NA 7 0.291 0.861 1.603
> 1BM NA 8 0.845 0.979 2.444
> 1BM C1 9 1.834 0.830 2.413
> 1BM H1 10 1.844 0.003 1.938
> 1BM H1 11 1.443 1.743 2.290
> 1BM C2 12 1.917 1.355 1.566
> 1BM HC 13 1.404 2.327 1.676
> 1BM HC 14 1.558 1.096 0.699
> 1BM CS 15 2.661 1.364 2.237
> 1BM HC 16 2.317 0.518 1.479
> 1BM HC 17 2.099 2.175 2.002
> 1BM CT 18 2.036 1.892 0.626
> 1BM HC 19 2.109 2.565 1.277
> 1BM HC 20 2.648 1.892 1.400
> 1BM HC 21 2.494 1.027 0.829
> 1BM C1 22 0.417 2.454 1.333
> 1BM H1 23 0.484 1.849 2.126
> 1BM H1 24 0.182 1.535 0.847
> 1BM H1 25 1.280 2.539 0.925
> 2Cl Cl 26 2.580 2.241 2.823
>
> ################# minimum.mdp ############################
> ; minim.mdp - used as input into grompp to generate em.tpr
>
> integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol = 10.0 ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep = 0.01 ; Energy step size
> nsteps = 500000 ; Maximum number of (minimization) steps to
> perform
> define = -DFLEXIBLE
>
> ; 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 = 1.0 ; Short-range electrostatic cut-off
> rvdw = 1.0 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>
> ########################## topol.top
> ########################################
>
> #include "oplsaa.ff/forcefield.itp"
>
>
> #include "ff_BM.itp"
> #include "BM.itp"
> #include "Cl.itp"
>
> ; Include water topology
> #include "oplsaa.ff/tip3p.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> [system]
> BM Cl
>
> [molecules]
> BM 1
> Cl 1
> SOL 857
>
--
==================================================
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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