[gmx-users] deformation in cnt
Atila Petrosian
atila.petrosian at gmail.com
Wed Dec 4 15:41:47 CET 2013
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.
------------------------------------------------------------------
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
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?
Please give me suggestions to solve deformation in cnt?
Any help will highly appreciated.
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