shivangi nangia wrote:
Dear Justin,
I have run into another problem.
I created the system by including DHB in vwdradii.dat as follows:
; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.
; longest matches are used
; '???' or '*' matches any residue name
; 'AAA' matches any protein residue name
??? C 0.15
??? F 0.12
??? H 0.04
??? N 0.110
??? O 0.105
??? S 0.16
*DHB C 0.5
DHB H 0.5
DHB O 0.5*
; Water charge sites
SOL MW 0
SOL LP 0
; Masses for vsite construction
GLY MN1 0
GLY MN2 0
ALA MCB1 0
ALA MCB2 0
VAL MCG1 0
VAL MCG2 0
ILE MCG1 0
ILE MCG2 0
ILE MCD1 0
ILE MCD2 0
LEU MCD1 0
LEU MCD2 0
MET MCE1 0
MET MCE2 0
TRP MTRP1 0
TRP MTRP2 0
THR MCG1 0
THR MCG2 0
LYSH MNZ1 0
LYSH MNZ2 0
After making this change, DHB molecules were not over lapping with each
other.
I tried to energy minimized the system.
minim.mdp
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
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
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
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)
constraints = none
After about 6000 steps the run stops with the message:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
Steepest Descents converged to machine precision in 6012 steps,
but did not reach the requested Fmax < 10.
Potential Energy = 1.0655116e+05
Maximum force = 1.6512177e+02 on atom 2076
Norm of force = 6.5337501e+00
The potential energy is high, but I still continued to equilibration.
After NVT equilibration, NVT equilbration runs into the following error
as soon it starts:
Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which
is larger than the 1-4 table size 2.000 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
/var/spool/pbs/mom_priv/jobs/1869547.lionxj.rcc.psu.edu.SC
<http://1869547.lionxj.rcc.psu.edu.SC>: line 14: 2359 Segmentation
fault mdrun -deffnm npt
So, I have three questions:
1. Is the starting structure bad?
Probably.
2. Did I change the vdwd radii by a lot (0.105 to 0.5)
Yes. And you shouldn't use those artificial values for anything else. Remove
them after you've inserted the DHB into your system. This is, of course, no
guarantee that the system is stable, either.
3. What value of table extension should be used for 1-4 interaction (
default value is?) if thats the problem to be fixed.
Do not adjust the table extension. If the system is blowing up, there's no
reason to troubleshoot the constraints; they're not your problem.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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