[gmx-users] Very high energies after energy minimization
Justin Lemkul
jalemkul at vt.edu
Wed Jul 27 22:19:02 CEST 2016
On 7/27/16 3:41 PM, Deep Bhattacharya wrote:
> Hello Evan,
>
> I am using the SPC solvent model.
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> Posre.itp from pdb2gmx for the protein
> ; In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
>
> [ position_restraints ]
> ; atom type fx fy fz
> 1 1 1000 1000 1000
> 5 1 1000 1000 1000
> 6 1 1000 1000 1000
> 7 1 1000 1000 1000
> 8 1 1000 1000 1000
> 9 1 1000 1000 1000
> 10 1 1000 1000 1000
> Cut out the initial part, remains constant throughout the same.
>
> Please suggest what changes can I do.
>
mdrun tells you that an absurd force is acting on atom 1553. Open up the
structure in your favorite visualization software and start looking there.
Beyond that, follow
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
Try minimizing the protein alone, the ligand alone, etc. until you spot where
the problem comes from.
-Justin
> Sincerely,
> Deep Bhattacharya
>
> On Wed, Jul 27, 2016 at 2:35 PM, Evan Lowry <evanwlowry at gmail.com> wrote:
>
>> Something is seriously wrong with the system. Do you have a solvent? If so,
>> use a trajectory viewer to ensure that there aren't solvent molecules on
>> top of your protein for some reason. Otherwise, it is probably related to
>> the protein structure clashing with itself (e.g., atoms are too close or
>> charges are incorrect). Additionally, what is in your positional restraint
>> file? Maybe you are arbitrarily restraining things that shouldn't be
>> restrained. Those are some things to check.
>>
>> Evan L.
>>
>> On Wed, Jul 27, 2016 at 1:04 PM, Deep Bhattacharya <
>> hypergenetics at gmail.com>
>> wrote:
>>
>>> Hello,
>>>
>>> I am attempting in performing energy minimization on protein-carbohydrate
>>> complex and I have obtained
>>> *Energy minimization has stopped, but the forces have not converged to
>> the*
>>> *requested precision Fmax < 1000 (which may not be possible for your
>>> system).*
>>> *It stopped because the algorithm tried to make a new step whose size was
>>> too*
>>> *small, or there was no change in the energy since last step. Either way,
>>> we*
>>> *regard the minimization as converged to within the available machine*
>>> *precision, given your starting configuration and EM parameters.*
>>> *You might need to increase your constraint accuracy, or turn*
>>> *off constraints altogether (set constraints = none in mdp file)*
>>>
>>> *Steepest Descents converged to machine precision in 193 steps,*
>>> *but did not reach the requested Fmax < 1000.*
>>> *Potential Energy = -2.25884936387141e+13*
>>> *Maximum force = 3.70136760562579e+25 on atom 1553*
>>> *Norm of force = 2.39587460988866e+23*
>>>
>>>
>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>> *define = -DPOSRES -DPOSRES_LIGAND*
>>> *integrator = steep *
>>> *emtol = 1000.0 *
>>> *emstep = 0.001 *
>>> *nsteps = 50000 *
>>> *energygrps = System*
>>> *nstlist = 1*
>>> *constraints = none*
>>> *; Parameters describing how to find the neighbors of each atom and how
>> to
>>> calculate the interactions*
>>> * ; 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 ; long range electrostatic cut-off*
>>> *rvdw = 1.0 ; long range Van der Waals cut-off*
>>> *pbc = xyz ;Periodic Boundary Conditions (yes/no)*
>>> *em.mdp*
>>>
>>> The maximum force seems unrealistic, how can I solve this issue?
>>> I have substituted charges of my ligand using atomicchargecalculator
>> (DOI:
>>> 10.1186/s13321-015-0099-x-- ) in the original file from PRODRG server.
>>> After reading many posts I can infer that there might be come problem in
>>> the topology of the ligand or the protein but I am not to recognize the
>>> actual source of the problem because if I go ahead with NPT and NVT
>>> equilibration my system is just exploding.
>>>
>>> Please help.
>>> Thanks in advance.
>>> *Deep S Bhattacharya*
>>> *Graduate Research Assistant*
>>> Mohs Biomedical Imaging & Nanotechnology Group
>>> Pharmaceutical Sciences
>>> *University of Nebraska Medical Center*
>>> 4018 Eppley Science Hall | Omaha, NE 68198-6805
>>> office 402.559.4349 | cell 402.906.1640
>>> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
>>> --
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>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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