[gmx-users] Reducing density using -vdwd option for a new solvent in the system
shivangi nangia
shivangi.nangia at gmail.com
Wed Jun 15 21:12:53 CEST 2011
Hello Justin and everybody,
I created a system of charged polyhistdine, counter anions and just 1 DHB
molecule is a box without making any change in the vdwradii.dat file.
This system does not energy minimize, it stops with the same 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.
What can be done to fix this problem?
The part of DHB itp file is:
[ moleculetype ]
; Name nrexcl
DHB 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 DHB OAA 1 -0.567 15.9994
2 C 1 DHB CAH 1 1.135 12.0110
3 OM 1 DHB OAD 1 -0.568 15.9994
4 C 1 DHB CAK 2 -0.004 12.0110
5 CR1 1 DHB CAG 2 0.004 12.0110
6 HC 1 DHB HAG 2 0.033 1.0080
7 C 1 DHB CAI 2 0.141 12.0110
8 OA 1 DHB OAB 2 -0.179 15.9994
9 H 1 DHB HAB 2 0.005 1.0080
10 CR1 1 DHB CAE 3 0.000 12.0110
11 HC 1 DHB HAE 3 0.000 1.0080
12 CR1 1 DHB CAF 3 0.000 12.0110
13 HC 1 DHB HAF 3 0.000 1.0080
14 C 1 DHB CAJ 4 0.082 12.0110
15 OA 1 DHB OAC 4 -0.113 15.9994
16 H 1 DHB HAC 4 0.031 1.0080
If I have the water/methanol or water:methanol in the system as the solvent,
the system runs fine.
Please help.
Thanks,
SN
On Tue, Jun 14, 2011 at 3:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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