[gmx-users] OPLS force field issue....

Wed Feb 5 03:51:20 CET 2014

yes it worked. i only added CA CA CZ CZ 0.000 0.000 0.000 0.000 in diheadral
block. since  all 12 errors point the same kind of diheadral type.

Then i tried to mdrun...i got this error message....

Fatal error:
1 particles communicated to PME node 6 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.

so i followed the  energy minimization steps given in the lysozyme
tutorial...

and ended up with vales like below...

 Steepest Descents converged to Fmax < 1000 in 56 steps
Potential Energy  =  8.3839850e+02
Maximum force     =  9.7320355e+02 on atom 206
Norm of force     =  1.8842863e+02

there you have clearly stated that the potential energy should be in range
of e-5 to e-6. but mine is ~+1000. i played with emsteps and
nsteps. but still am getting the same potential energy.

could you please help me out with this?

Thank you!

minimum.mdp i used-( taken from your lysozyme tutorial)

 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          = 0.0001         ; Energy step size
nsteps          = 50000000              ; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist         = 1.0   ; 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)
~

Sidath

On Tue, Feb 4, 2014 at 8:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/3/14, 10:14 PM, Sidath Wijesinghe wrote:
>
>> Justin,,
>>
>> i rechecked the opls/ff that i used and found some errors, after
>> correction them
>> i got the .top file.
>> note that i was able to define the charge groups as well. when i use this
>> .top
>> file with grompp,
>> now am getting 12 errors...as follwos..
>>
>>
>> ERROR 1 [file topol.top, line 1399]:
>>    No default Ryckaert-Bell. types
>>
>>
>> ERROR 2 [file topol.top, line 1400]:
>>    No default Ryckaert-Bell. types
>>
>>
>> ERROR 3 [file topol.top, line 1415]:
>>    No default Ryckaert-Bell. types
>>
>>
>> ERROR 4 [file topol.top, line 1416]:
>>    No default Ryckaert-Bell. types
>> and so on...
>>
>> i did the mapping as you suggested,as an example line 1399 in .top
>> as follwos...
>>   2     1    82    81     3  ( here 2 1 82 & 81 are carbon atoms)
>>
>> and the mapping to all 12 errors.....then  modified the ffbonded.itp
>> file's
>> diheadral block as follows...
>>
>> C2     C1    C82    C81       3    0.00  0.00 0.00 0.00
>>
>> so on....
>>
>> then bond tyype block as follows....
>>
>> C2     C1      1 0.00 0.00... so on....
>>
>> added those atom types in atomtypes.atp like below...
>> C1
>> C2
>> C3
>> C4
>> C11
>> C12
>> C13................so on
>>
>> after that when i do grompp  gives me a fatal error like
>>
>> Program grompp, VERSION 4.5.5
>> Source code file: toppush.c, line: 631
>>
>> Fatal error:
>> Unknown bond_atomtype C1
>>
>> could you please tell me what i have done wrong?
>>
>>
> You used atom names, not atom types.  In [atoms] in your .top, each atom
> type is assigned as opls_XXX.  Looking in ffnonbonded.itp, the second
> column of the corresponding opls_XXX type is its bonded type equivalent.
>  That is the identifier you need to be using.  The force field doesn't care
> what atoms are named, but it does care what type they are.
>
>
>  and at the same time....i tied delete those 12 lines in .top and do
>> grompp...it
>> worked....but when i
>> did mdrun.....i am getting the signs of blowing up system....what i can
>> do over
>> here....how can i get rid of these errors
>> and carry out my simulation?
>>
>>
> Of course if you delete an essential bonded interaction, the simulation
> will go haywire.  Deletion may be convenient for getting grompp to shut up,
> but it's not sound practice.
>
> -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
> http://mackerell.umaryland.edu/~jalemkul
>
>
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-- 
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University