[gmx-users] deformation in cnt
Justin Lemkul
jalemkul at vt.edu
Wed Dec 4 16:17:41 CET 2013
On 12/4/13 9:41 AM, Atila Petrosian wrote:
> Dear gromacs users
>
> My system contains protein + cnt + water molecules (system.gro).
>
> cnt is infinite and z dimension of box is equal to the length of
> the cnt axis.
>
Is it exactly equal to the size of the CNT, or is there sufficient space for the
periodic bonded interactions? The box size should be (length of CNT) + (bond
length).
> ------------------------------------------------------------------
> em.mdp file is as follows:
>
> integrator = steep
> nsteps = 10000
> nstcomm = 1
> emtol = 500
> emstep = 0.01
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> vdwtype = Cut-off
> rcoulomb = 1.0
> rvdw = 1.0
> tcoupl = no
> pcoupl = no
> gen_vel = no
> constraints = none
> periodic_molecules = yes
> ------------------------------------------------------------------
> When I used:
>
> grompp -f em.mdp -c system.gro -p all.top -o em.tpr
> mdrun -deffnm em -v
>
> Minimization was converged truly.
> Steepest Descents converged to Fmax < 500 in 9623 steps
> Potential Energy = -6.7001516e+04
> Maximum force = 4.6945612e+02 on atom 490
> Norm of force = 8.2927048e+01
>
> The curve of potential energy vs step is normal (decrease of energy).
>
> When I saw em.gro by vmd, both ends of cnt were deformed. The figure
> is in following link:
>
> https://www.dropbox.com/s/v1gczzxnyu6jizf/em.docx
>
The deformation suggests very large bonded forces that would arise from an
incorrect box size.
>
> Then I used:
>
> grompp -f nvt.mdp -c em.gro -p all.top -o nvt.tpr -n index1.ndx
> mdrun -deffnm nvt -v
> ------------------------------------------------------------------
> nvt.mdp file is as follows:
>
> title = NVT equilibration
> define = -DPOSRES ; position restrain the protein and cnt
> integrator = md
> nsteps = 50000
> dt = 0.002
> nstxout = 100
> nstvout = 100
> nstenergy = 100
> nstlog = 100
> continuation = no
> constraint_algorithm = Lincs
> constraints = all-bonds
> lincs_iter = 1
> lincs_order = 4
> ns_type = grid
> nstlist = 5
> rlist = 1.2
> rcoulomb = 1.2
> rvdw = 1.2
> coulombtype = PME
> pme_order = 4
> fourierspacing = 0.16
> tcoupl = V-rescale
> tc-grps = Protein CNT Water_Ion
> tau_t = 0.1 0.1 0.1
> ref_t = 310 310 310
> pcoupl = no
> pbc = xyz
> periodic_molecules = yes
> DispCorr = EnerPres
> gen_vel = yes
> gen_temp = 300
> gen_seed = -1
> ------------------------------------------------------------------
> I had following notes:
>
> NOTE: Periodic molecules are present in this system. Because of this,
> the domain decomposition algorithm cannot easily determine the
> minimum cell size that it requires for treating bonded interactions.
> Instead, domain decomposition will assume that half the non-bonded
> cut-off will be a suitable lower bound.
>
> NOTE: Turning on dynamic load balancing
>
> mdrun was completed and nvt.gro file was created. When I saw this file
> by vmd, cnt was deformed again.
>
> I calculated Temperature using g_energy:
>
> Energy Average Err.Est. RMSD Tot-Drift
> --------------------------------------------------------------------
> Temperature 309.373 0.29 4.38465 1.81888 (K)
>
>
>
> -----------------------------------------------------------------------
> -----------------------------------------------------------------------
>
> *** To solve this problem, I add following parameters to em.mdp file,
>
> freezegrps = CNT
> freezedim = Y Y Y
>
> Minimization was converged truly. The curve of potential energy
> vs step is normal (decrease of energy). This time, when I saw em.gro
> by vmd, there is no deformation in em.gro. All things is right.
>
> Then I used:
>
> grompp -f nvt.mdp -c em.gro -p all.top -o nvt.tpr -n index1.ndx
> mdrun -deffnm nvt -v
>
> I encountered fatal errro:
>
> NOTE: Periodic molecules are present in this system. Because
> of this, the domain decomposition algorithm cannot easily determine
> the minimum cell size that it requires for treating bonded
> interactions. Instead, domain decomposition will assume that half
> the non-bonded cut-off will be a suitable lower bound.
>
> Making 1D domain decomposition 2 x 1 x 1
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.357970, max 1.843173 (between atoms 529 and 307)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 611 589 159.4 0.1181 0.0589 0.1418
> 612 610 159.6 0.1183 0.0586 0.1418
> 373 372 158.3 0.1199 0.0637 0.1418
> .
> .
> .
> Wrote pdb files with previous and current coordinates
> starting mdrun 'Protein'
> 50000 steps, 100.0 ps.
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.283837, max 2.397211 (between atoms 528 and 308)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 611 589 49.1 0.1181 0.1440 0.1418
> 591 589 38.6 0.1467 0.1063 0.1418
> 612 610 47.0 0.1183 0.1373 0.1418
> .
> .
> .
> Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.1#
>
> Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.1#
> Wrote pdb files with previous and current coordinates
> step 0
> Step 1, time 0.002 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 4.477828, max 18.922325 (between atoms 263 and 262)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 592 565 32.2 0.1540 0.1604 0.1418
> 590 589 176.1 0.0926 2.1198 0.1418
> 613 591 175.5 0.1709 0.6760 0.1418
> .
> .
> .
> Wrote pdb files with previous and current coordinates
> Warning: 1-4 interaction between 282 and 453 at distance 2.488
> which is larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> Step 2, time 0.004 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 271056830546.133942, max 2821136056320.000000 (between atoms 564 and
> 562)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 592 565 139.8 0.1604 32700858368.0000 0.1418
> 566 565 71.6 0.1761 28682631168.0000 0.1418
> 615 593 42.1 0.1566 37479.4609 0.1418
> 595 593 91.2 0.1507 7612.9775 0.1418
> 594 593 133.2 0.1582 2063502848.0000 0.1418
> 570 538 60.0 0.1409 0.6389 0.1418
> 539 538 63.4 0.1410 0.7026 0.1418
>
> step 2: Water molecule starting at atom 4008 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> 572 540 33.1 0.1411 0.2006 0.1418
> 594 567 113.9 0.1530 2063502848.0000 0.1418
> 569 567 50.9 0.1449 2572.7451 0.1418
> 568 567 66.4 0.1509 778853888.0000 0.1418
> 596 569 122.1 0.1417 197.0946 0.1418
> 570 569 118.5 0.1413 197.1465 0.1418
> .
> .
> .
> step 2: Water molecule starting at atom 3957 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.6
> Source code file: pme.c, line: 538
>
> Fatal error:
> 3 particles communicated to PME node 1 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> What is reason of notes and error?
>
The fatal error arises because you froze the CNT during EM. The original
results show clearly that there are massive forces at the box boundaries that
are dissipated throughout the structure, giving rise to the distortion. By
freezing the CNT, you prevented the relaxation of those forces, so as soon as
dynamics started, the structure crumbled and the system collapsed.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
==================================================
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