[gmx-users] How to avoid the infinite potential energy in simulations of dimers?
Justin Lemkul
jalemkul at vt.edu
Sat Feb 22 19:49:12 CET 2020
On 2/21/20 1:01 PM, Qing Liu wrote:
> Dear Justin Lemkul,
>
> Thanks for your reply. I just downloaded the Cryo-EM structure of the dimer from RCSB, added missing residues using Modeller and built systems by the following commands:
>
>
>
> gmx pdb2gmx -f dimer.pdb -o dimer.gro -p dimer.top -water tip3p -ff amber99sb-ildn -ignh
> gmx editconf -f dimer.gro -o vac-min-pbc.gro -bt cubic -d 1.5 -c
> gmx solvate -cp vac-min-pbc.gro -cs spc216.gro -p dimer.top -o vac-min-pbc-solv.gro
> gmx grompp -v -f sol-min.mdp -c vac-min-pbc-solv.gro -p dimer.top -o vac-min-pbc-solv.tpr
> gmx genion -s vac-min-pbc-solv.tpr -o vac-min-pbc-solv-salt.gro -conc 0.15 -neutral -pname NA -nname CL -p dimer.top
> gmx grompp -f sol-min.mdp -c vac-min-pbc-solv-salt.gro -p dimer.top -o vac-min-pbc-solv-salt-min.tpr
> gmx mdrun -v -deffnm vac-min-pbc-solv-salt-min
> gmx grompp -f pr-md.mdp -c vac-min-pbc-solv-salt-min.gro -p dimer.top -o pr-md.tpr -r vac-min-pbc-solv-salt-min.gro
> gmx mdrun -nb gpu -v -deffnm pr-md
>
>
> The contents of sol-min.mdp file are:
>
>
> ; Define can be used to control processes
> define = -DFLEXIBLE
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol
> nsteps = 5000 ; Maximum number of (minimization) steps to perform
> nstenergy = 1 ; Write energies to disk every nstenergy steps
> energygrps = System ; Which energy group(s) to write to disk
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> coulombtype = cut-off ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0 ; long range electrostatic cut-off
> rvdw = 1.0 ; long range Van der Waals cut-off
> constraints = none ; Bond types to replace by constraints
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
> sc-coul = yes
>
>
>
> The log file of energy minimization shows:
> Steepest Descents converged to machine precision in 2108 steps,
> but did not reach the requested Fmax < 1.
> Potential Energy = -2.0181694e+07
> Maximum force = 3.4778253e+02 on atom 114839
> Norm of force = 3.9966155e+01
>
>
> The contents of pr-md.mdp are:
> title = PR MD
> define =-DPOSRES
> ;run control
> integrator =md
> tinit =0
> dt =0.002
> nsteps =500000
> comm_mode =Linear
> nstcomm =10
> comm_grps =System
> ;output control
> nstxout =0
> nstvout =0
> nstlog =50000
> nstcalcenergy =1
> nstenergy =50000
> nstxtcout =50000
> xtc_grps =System
> energygrps =System
> ;neighbor searching
> nstlist =10
> ns_type =grid
> pbc =xyz
> rlist =1.4
> ;electrostatics
> coulombtype =PME
> rcoulomb =1.4
> ;vdw
> vdwtype =Cut-off
> rvdw =1.4
> dispCorr =EnerPres
> ;Ewald
> fourierspacing =0.1
> pme_order =4
> ewald_rtol =1e-5
> ;temperature coupling
> tcoupl =v-rescale
> tc_grps =System
> tau_t =0.1
> ref_t =200
> ;velocity generation
> gen-vel =no
> ;bonds
> constraints =all-bonds
> constraint_algorithm =SHAKE
> shake-tol =0.0001
> morse =no
> continuation =yes
> sc-coul =yes
>
>
>
> The pr-md.log shows:
>
> Fatal error:
> Step 2460: The total potential energy is nan, which is not finite. The LJ and
> electrostatic contributions to the energy are 3.25168e+06 and -1.99067e+07,
> respectively. A non-finite potential energy can be caused by overlapping
> interactions in bonded interactions or very large or Nan coordinate values.
> Usually this is caused by a badly- or non-equilibrated initial configuration,
> incorrect interactions or parameters in the topology.
>
>
You're changing cutoffs, treatment of constraints, etc. at various
points in your protocol. Don't do that. Be consistent. You probably have
a water molecule that got stretched too far via -DFLEXIBLE and now it
can't be constrained properly.
-Justin
>
>
>
>
>
> --
>
>
> Best wishes,
>
> ------------------------------------------------------------
>
> Qing Liu
>
> Fudan Univ.
>
> Mobile: +86—13358129621
>
> E-mail: 15110700076 at fudan.edu.cn
>
>
>
>
>
>
>> Message: 5
>> Date: Fri, 21 Feb 2020 09:21:34 -0500
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] How to avoid the infinite potential energy in
>> simulations of dimers?
>> Message-ID: <b1dbc8bb-8640-5834-dd59-9a69a98e591a at vt.edu>
>> Content-Type: text/plain; charset=gbk; format=flowed
>>
>>
>>
>> On 2/21/20 5:11 AM, Qing Liu wrote:
>>> Dear Gromacs users,
>>> I run some simulations of dimers, a protein binding another protein. When these simulations step into equilibriumstages, they will crash with the following:
>>>
>>>
>>>
>>>
>>>
>>> Step 2029: The total potential energy is nan, which is not finite. The LJ and
>>> electrostatic contributions to the energy are 746119 and -5.71229e+06,
>>> respectively. A non-finite potential energy can be caused by overlapping
>>> interactions in bonded interactions or very large or Nan coordinate values.
>>> Usually this is caused by a badly- or non-equilibrated initial configuration,
>>> incorrect interactions or parameters in the topology.
>>>
>>>
>>> I try to turn on soft-core potential but it's not working. However, the simulations of monomers with same mdp files are normal. How should I do to solve the problem?
>>>
>> Your initial configuration is unreasonable as you have a massive LJ
>> repulsion. How did you construct the coordinates of the system? Likely
>> energy minimization will have reported unreasonable forces, as well.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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