[gmx-users] Reducing density using -vdwd option for a new solvent in the system
shivangi nangia
shivangi.nangia at gmail.com
Tue Jun 14 21:10:08 CEST 2011
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: line 14: 2359
Segmentation fault mdrun -deffnm npt
So, I have three questions:
1. Is the starting structure bad?
2. Did I change the vdwd radii by a lot (0.105 to 0.5)
3. What value of table extension should be used for 1-4 interaction (
default value is?) if thats the problem to be fixed.
Please guide.
Thanks,
SN
On Tue, Jun 14, 2011 at 11:29 AM, shivangi nangia <shivangi.nangia at gmail.com
> wrote:
> Thanks Justin, vdwradii.dat suggestion worked :)
>
>
>
>
> On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul <jalemkul at vt.edu>wrote:
>
>>
>>
>> shivangi nangia wrote:
>>
>>> Hello dear gmx-users,
>>>
>>> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as
>>> the solvent ( with a positively charged protein and few DHB anions) in a
>>> box.
>>>
>>> I have created the .itp and .gro file of DHB using PRODRG.
>>>
>>>
>> Unrelated advice - the topology is probably useless unless you've
>> corrected the charges. See the paper linked from:
>>
>> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>>
>>
>> I am able to create the system, but when I try to energy minimize the
>>> system I get the message:
>>>
>>> Steepest Descents:
>>> Tolerance (Fmax) = 1.00000e+01
>>> Number of steps = 50000
>>> Step= 14, Dmax= 1.2e-06 nm, Epot= 9.04353e+19 Fmax= inf, atom=
>>> 2781
>>> 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.
>>>
>>> writing lowest energy coordinates.
>>>
>>> Back Off! I just backed up em.gro to ./#em.gro.1#
>>>
>>> Steepest Descents converged to machine precision in 15 steps,
>>> but did not reach the requested Fmax < 10.
>>> Potential Energy = 9.0435262e+19
>>> Maximum force = inf on atom 2781
>>> Norm of force = inf
>>>
>>>
>>> The reason behind this was that DHB molecules were on top of each other,
>>> highly dense system ( viewed in VMD)
>>> So, to reduce the density of DHB molecules, I tried using-vdwd option of
>>> genbox (changed from default value of 0.105 to 0.5)
>>> But, I got almost same number of DHB molecules using genbox.
>>>
>>>
>> The -vdwd option has no effect unless you're using atom names that are not
>> found in vdwradii.dat (see the genbox help description). Your DHB molecule
>> should be unaffected by the use of -vdwd.
>>
>>
>>
>>> What is the best solution to this problem as I understand, reducing the
>>> density of DHB molecules around the protein as a solvent or there is some
>>> other problem?
>>>
>>>
>> You need to generate a configuration in which molecules aren't
>> overlapping. There are several ways to accomplish this. You can manually
>> place molecules within a box at a desired location with editconf -center,
>> otherwise genbox -ci -nmol. If the locations of the molecules are not what
>> you desire with genbox, change the value of -seed and try again.
>>
>> -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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110614/e3352b37/attachment.html>
More information about the gromacs.org_gmx-users
mailing list