[gmx-users] segementation fault- water molecule can not be settled- free mdrun error (repica exchange)
Guo, Yanan
yanan.guo at partner.kit.edu
Mon Jan 13 14:46:47 CET 2014
Dear Justin,
Thanks a lot for your help.
According to your suggestion, I changed my pressure coupling settings:
; Pressure coupling
pcoupl = no
pcoupltype = isotropic
tau_p = 2.0
ref_p =
compressibility =
Then there is no “segementation fault”.Thank you very much! (I also made a test by reducing the time step, but it didn't work.)
But I have a question here. Given the whole protocol of my simulation:
1. energy minimization of the system
2. position restrained equilibration of the system in NVT ensemble and NPT ensemble.
3. free MD simulation (replica exchange and simulated annealing)
To avoid the collapse of the system with a sudden relax, I released the position restraints step by step in NPT ensemble before free MD simulation. So I am wondering is it proper to turn off the pressure coupling (pcoupl = 0) in a free MD simulation? Especially in the case that I want to treat this free MD as the production MD simulation? Or we cann't use replica exchange as a production MD simulation?
Thank you very much!
Best
Yanan
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of gromacs.org_gmx-users-request at maillist.sys.kth.se [gromacs.org_gmx-users-request at maillist.sys.kth.se]
Sent: Sunday, January 12, 2014 4:53 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 117, Issue 25
Send gromacs.org_gmx-users mailing list submissions to
gromacs.org_gmx-users at maillist.sys.kth.se
To subscribe or unsubscribe via the World Wide Web, visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
gromacs.org_gmx-users-request at maillist.sys.kth.se
You can reach the person managing the list at
gromacs.org_gmx-users-owner at maillist.sys.kth.se
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."
Today's Topics:
1. segementation fault- water molecule can not be settled- free
mdrun error (repica exchange) (Guo, Yanan)
2. Fw: NVT equilibration (kiana moghaddam)
3. Re: LIE method (Justin Lemkul)
4. Re: Fw: NVT equilibration (Justin Lemkul)
5. Re: segementation fault- water molecule can not be settled-
free mdrun error (repica exchange) (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Sun, 12 Jan 2014 14:09:00 +0100
From: "Guo, Yanan" <yanan.guo at partner.kit.edu>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] segementation fault- water molecule can not be
settled- free mdrun error (repica exchange)
Message-ID:
<4E17E35DDBA53647900414DE795626BE5E732912B3 at KIT-MSX-07.kit.edu>
Content-Type: text/plain; charset="Windows-1252"
Hello everyone,
The procedure that I performed my MD simulation is as follows:
1. pdb2gmx?
2. editconf?
3. genbox?
4. genion?
5. energy minimization?
6. equilibration, to release the position restraints step by step
firstly, equilibration in temperature phase (force on each atom in three axis is 1000)
secondly, equilibration in pressure phase (force on each atom in three axis is 100)
thirdly, equilibration in pressure phase (force on each atom in three axis is 10)
7. replica exchange and simulated annealing (I would like to use this replica exchange or simulated annealing as the production MD simulation)
Part of the error file of replica exchange:
step 502: Water molecule starting at atom 29883 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 502: Water molecule starting at atom 35217 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 502: Water molecule starting at atom 36021 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 502: Water molecule starting at atom 12588 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
step 502: Water molecule starting at atom 24726 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
??
??
??
End of error message ***
[ic2n113:43048] *** Process received signal ***
[ic2n113:43048] Signal: Segmentation fault (11)
[ic2n113:43048] Signal code: Address not mapped (1)
[ic2n113:43048] Failing at address: 0x2aeb1fa73054
[ic2n113:43067] *** Process received signal ***
[ic2n113:43067] Signal: Segmentation fault (11)
[ic2n113:43067] Signal code: Address not mapped (1)
[ic2n113:43067] Failing at address: 0x2b2b1f0707d0
The mdp file for replica exchange (the only difference among the replicas is the ref_t value)
Run parameters
integrator = md
nsteps = 200000000
dt = 0.001
; Output control
nstxout = 0
nstvout = 0
nstfout = 0
nstxtcout = 10000
nstenergy = 10000
nstlog = 10000
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
; Temperature coupling is on
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300.00 300.00
; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
; Periodic boundary conditions
pbc = xyz
; Dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = no
What confuses me is that, there is no such error for the simulated annealing.
There is no other difference between my sa.mdp and repl.mdp file except that sa.mdp contains the parameters of annealing.
Any help and suggestion are appreciated.
Thank you very much!
Greetings
Yanan
------------------------------
Message: 2
Date: Sun, 12 Jan 2014 07:22:18 -0800 (PST)
From: kiana moghaddam <ki_moghaddam at yahoo.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] Fw: NVT equilibration
Message-ID:
<1389540138.40289.YahooMailNeo at web160401.mail.bf1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Dear Justin
I absolutely know that this equilibration and heating are suitable for my system, but I want to sure whether the other parameters for example?ref_t =300 is correct or not. Maybe it is true that 100ps run?is very very faster than your email, but?reliable answer is?more important than lag time.?
------------------------------
Message: 3
Date: Sun, 12 Jan 2014 10:49:11 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] LIE method
Message-ID: <52D2B977.3080300 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 1/12/14, 12:03 AM, Mahboobeh Eslami wrote:
> dear Justin thanks for your reply
> is the rerun energies needed only for protein ligand complex? do the ligand in
> water simulation need the rerun energies?
Both. It wouldn't make sense to re-calculate energies from one PME system, then
try to take the difference of the energies from another system where the same
correction hasn't been applied.
-Justin
> thanks a lot
>
>
> On Sunday, January 12, 2014 1:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/11/14, 2:07 AM, Mahboobeh Eslami wrote:
> > hi dear GMX users
> > I simulated protein-ligand complex for 20 nanoseconds. I want to calculate
> free energy by LIE method so I simulated ligand in water in the same conditions.
> I used PME and full periodic boundary conditions in my simulations so I wrote a
> new .mdp file that didn't use PME (I used cut off) and used following command
> for protein-ligand complex simulation:
> > mdrun -s newtpr.tpr -rerun full20ns.xtc
> > then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command.
> > are these steps sufficient. is the stage or another commandnecessary?
>
>
> If the protein-ligand simulation was done with PME as well, then you need to get
> the rerun energies, as well.
>
> -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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
>
> ==================================================
>
>
--
==================================================
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
==================================================
------------------------------
Message: 4
Date: Sun, 12 Jan 2014 10:49:35 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org, kiana moghaddam <ki_moghaddam at yahoo.com>
Subject: Re: [gmx-users] Fw: NVT equilibration
Message-ID: <52D2B98F.3040505 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 1/12/14, 10:22 AM, kiana moghaddam wrote:
> Dear Justin
>
>
>
> I absolutely know that this equilibration and heating are suitable for my system, but I want to sure whether the other parameters for example ref_t =300 is correct or not. Maybe it is true that 100ps run is very very faster than your email, but reliable answer is more important than lag time.
>
ref_t is irrelevant during annealing.
-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
==================================================
------------------------------
Message: 5
Date: Sun, 12 Jan 2014 10:51:50 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] segementation fault- water molecule can not
be settled- free mdrun error (repica exchange)
Message-ID: <52D2BA16.40508 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 1/12/14, 8:09 AM, Guo, Yanan wrote:
> Hello everyone,
>
> The procedure that I performed my MD simulation is as follows:
>
>
> 1. pdb2gmx?
>
> 2. editconf?
>
> 3. genbox?
>
> 4. genion?
>
> 5. energy minimization?
>
> 6. equilibration, to release the position restraints step by step
>
> firstly, equilibration in temperature phase (force on each atom in three axis is 1000)
>
> secondly, equilibration in pressure phase (force on each atom in three axis is 100)
>
> thirdly, equilibration in pressure phase (force on each atom in three axis is 10)
>
> 7. replica exchange and simulated annealing (I would like to use this replica exchange or simulated annealing as the production MD simulation)
>
>
>
> Part of the error file of replica exchange:
>
>
>
> step 502: Water molecule starting at atom 29883 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 502: Water molecule starting at atom 35217 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 502: Water molecule starting at atom 36021 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 502: Water molecule starting at atom 12588 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 502: Water molecule starting at atom 24726 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> ??
>
> ??
>
> ??
>
> End of error message ***
>
> [ic2n113:43048] *** Process received signal ***
>
> [ic2n113:43048] Signal: Segmentation fault (11)
>
> [ic2n113:43048] Signal code: Address not mapped (1)
>
> [ic2n113:43048] Failing at address: 0x2aeb1fa73054
>
> [ic2n113:43067] *** Process received signal ***
>
> [ic2n113:43067] Signal: Segmentation fault (11)
>
> [ic2n113:43067] Signal code: Address not mapped (1)
>
> [ic2n113:43067] Failing at address: 0x2b2b1f0707d0
>
>
>
>
>
> The mdp file for replica exchange (the only difference among the replicas is the ref_t value)
>
> Run parameters
>
> integrator = md
>
> nsteps = 200000000
>
> dt = 0.001
>
> ; Output control
>
> nstxout = 0
>
> nstvout = 0
>
> nstfout = 0
>
> nstxtcout = 10000
>
> nstenergy = 10000
>
> nstlog = 10000
>
> ; Bond parameters
>
> continuation = yes
>
> constraint_algorithm = lincs
>
> constraints = all-bonds
>
> lincs_iter = 1
>
> lincs_order = 4
>
> ; Neighborsearching
>
> ns_type = grid
>
> nstlist = 5
>
> rlist = 1.0
>
> rcoulomb = 1.0
>
> rvdw = 1.0
>
> ; Electrostatics
>
> coulombtype = PME
>
> pme_order = 4
>
> fourierspacing = 0.16
>
> ; Temperature coupling is on
>
> tcoupl = V-rescale
>
> tc-grps = Protein Non-Protein
>
> tau_t = 0.1 0.1
>
> ref_t = 300.00 300.00
>
> ; Pressure coupling is on
>
> pcoupl = Parrinello-Rahman
>
> pcoupltype = isotropic
>
> tau_p = 2.0
>
> ref_p = 1.0
>
> compressibility = 4.5e-5
>
> ; Periodic boundary conditions
>
> pbc = xyz
>
> ; Dispersion correction
>
> DispCorr = EnerPres
>
> ; Velocity generation
>
> gen_vel = no
>
>
>
> What confuses me is that, there is no such error for the simulated annealing.
>
>
>
> There is no other difference between my sa.mdp and repl.mdp file except that sa.mdp contains the parameters of annealing.
>
REMD under an NPT ensemble can be unstable. You may need to reduce your time
step or otherwise change the pressure coupling settings for the runs to be
stable. If the temperature range includes very high temperatures, NPT simply
may never be stable, because the exchanges between neighboring replicas will be
problematic.
-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
==================================================
------------------------------
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
End of gromacs.org_gmx-users Digest, Vol 117, Issue 25
******************************************************
More information about the gromacs.org_gmx-users
mailing list