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.
--
Best wishes,
------------------------------------------------------------
Qing Liu
Fudan Univ.
Mobile: +86—13358129621
E-mail: 15110700...@fudan.edu.cn
>Message: 5
>Date: Fri, 21 Feb 2020 09:21:34 -0500
>From: Justin Lemkul <jalem...@vt.edu>
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] How to avoid the infinite potential energy in
> simulations of dimers?
>Message-ID: <b1dbc8bb-8640-5834-dd59-9a69a98e5...@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
>
>jalem...@vt.edu | (540) 231-3129
>http://www.thelemkullab.com
>
>==================================================
--
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