[gmx-users] Re: gmx-users Digest, Vol 72, Issue 36
Ozge Engin
ozge.engin at gmail.com
Thu Apr 8 09:24:10 CEST 2010
Hi Ravi,
I had a similar problem to yours when I was dealing with simulation of a
peptide channel. I had the crystal structure of the channel consisting of
crystal water molecules and the peptide channel. I energy minimized the
system. Although nothing seems to be overlap, energy minimization crashed.
After that I decided to put each water molecule into the channel one by one,
and did energy minimization after each water molecule. If the energy
minimization did not crash, I continued adding another water molecule. If it
crashed I changed the location of the last water molecule in the channel.
But I am afraid you have much more water molecules than mine. I had more or
less 100 water molecules within the channel, and also note that I had not
any ions in the system.
Regards
On Thu, Apr 8, 2010 at 9:13 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. RE: energy minimization in charged systems (Dallas B. Warren)
> 2. Simulating a metal slab (radhika jaswal)
> 3. Re: Simulating a metal slab (Mark Abraham)
> 4. Re: position_restraint anfd full Dynamics and berendsen Nose
> hoover Thermostat (shahid nayeem)
> 5. Re:Re: g_nmeig_d error:cannot allocate region
> (sarbani chattopadhyay)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 08 Apr 2010 15:22:53 +1000
> From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
> Subject: RE: [gmx-users] energy minimization in charged systems
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <89907EA1DCFB7548A431C13A270F9DD509B823C5 at prk-exch-01.vcp.local>
> Content-Type: text/plain; charset=iso-8859-1
>
> What are the atoms that are causing the problems actually doing, where are
> they located etc?
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Ravi Bhadauria
> Sent: Thursday, 8 April 2010 3:11 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] energy minimization in charged systems
>
> Hi all,
>
> I am trying to simulate a electroosmotic flow in a nanochannel. System
> consists of water + (Cl-) ions in a channel confined of silicon <111> walls.
> I start with taking water as only solvent, equilibrating the system for
> about 12-15 ps (gmxcheck runs clean), and then use genion to insert (Cl-)
> ions. Walls are charged appropriately to maintain electro-neutrality in the
> system. The problem is with Energy minimization after inserting ions using
> steep algorithm (haven't turned on the electric field yet). I am getting an
> error like this:
>
> t = 0.038 ps: Water molecule starting at atom 2569 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
>
> and
>
> Steepest Descents converged to machine precision in 88 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy = 1.75456106043895e+06
> Maximum force = 1.07111309902475e+11 on atom 4898
> Norm of force = 1.48772609239112e+09
>
> If it were only couple of such molecules, I could have removed them easily
> from the gro file. The problem is twofold, there are around 10 molecules
> which give this error message, plus even after removal of these molecules,
> energy minimization results in the same error on different sets of
> molecules. I have tried a number of ways to tackle this including tuning the
> time step. Is there any way to avoid this? Any help would be appreciated.
>
> Thanks in advance.
>
> --
> Ravi Bhadauria
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 8 Apr 2010 11:17:15 +0530 (IST)
> From: radhika jaswal <jaswalradhika at yahoo.co.in>
> Subject: [gmx-users] Simulating a metal slab
> To: gmx-users at gromacs.org
> Message-ID: <109124.71315.qm at web94806.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hii Everybody...
>
>
>
> I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in
> length and 4-5 molecules wide just as to mimic a rigid metal slab for
> further interaction studies. Can gromacs library support this and how I
> can do that...
>
> All suggestions are welcome.
>
>
>
> Thanks
>
>
>
> Radhika
>
>
>
> Send free SMS to your Friends on Mobile from your Yahoo! Messenger.
> Download Now! http://messenger.yahoo.com/download.php
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> ------------------------------
>
> Message: 3
> Date: Thu, 08 Apr 2010 15:54:24 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Simulating a metal slab
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4BBD6F90.7080108 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 8/04/2010 3:47 PM, radhika jaswal wrote:
> > Hii Everybody...
> >
> > I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in
> > length and 4-5 molecules wide just as to mimic a rigid metal slab for
> > further interaction studies. Can gromacs library support this and how I
> > can do that...
>
> Yes, in principle. You will need a force field that supports such
> interactions, and GROMACS does not come with any. Your first place to
> look should be in the published literature for other simulations of such
> materials and such slabs. Don't assume GROMACS is the best tool for the
> task.
>
> Mark
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 8 Apr 2010 11:27:37 +0530
> From: shahid nayeem <msnayeem at gmail.com>
> Subject: Re: [gmx-users] position_restraint anfd full Dynamics and
> berendsen Nose hoover Thermostat
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <o2mea6f7fbe1004072257yedd75eebn7c8f2e714d14a6fc at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Please see the following pr.mdp and full.mdp
> pr.mdp
>
>
> cpp = /usr/bin/cpp
>
> define = -DPOSRES
>
> constraints = all-bonds
>
> integrator = md
>
> dt = 0.002 ; ps !
>
> nsteps = 50000 ; total 100 ps.
>
> nstcomm = 1
>
> nstxout = 500
>
> nstvout = 1000
>
> nstfout = 0
>
> nstlog = 10
>
> nstenergy = 10
>
> nstlist = 10
>
> ns_type = grid
>
> rlist = 1.0
>
> rcoulomb = 1.0
>
> rvdw = 1.0
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl = berendsen
>
> tc-grps = Protein Non-protein
>
> tau_t = 0.1 0.1
>
> ref_t = 500 500
>
> ; Energy monitoring
>
> energygrps = Protein Non-protein
>
> ; Pressure coupling is not on
>
> Pcoupl = no
>
> tau_p = 0.5
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> ; Generate velocites is on at 500 K.
>
> gen_vel = yes
>
> gen_temp = 500.0
>
> gen_seed = 173529
>
> full.mdp
>
> cpp = /usr/bin/cpp
>
> constraints = all-bonds
>
> integrator = md
>
> dt = 0.002 ; ps !
>
> nsteps = 50000000 ; total 100000 ps.
>
> nstcomm = 1
>
> nstxout = 5000
>
> nstvout = 40000
>
> nstfout = 0
>
> nstlog = 100
>
> nstenergy = 100
>
> nstlist = 10
>
> ns_type = grid
>
> rlist = 1.0
>
> rcoulomb = 1.0
>
> rvdw = 1.0
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl = berendsen
>
> tc-grps = Protein Non-protein
>
> tau_t = 0.1 0.1
>
> ref_t = 500 500
>
> ; Energy monitoring
>
> energygrps = Protein Non-protein
>
> ; Isotropic pressure coupling is now on
>
> Pcoupl = berendsen
>
> Pcoupltype = isotropic
>
> tau_p = 0.5
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> ; Generate velocites is off at 500 K.
>
> gen_vel = no
>
> gen_temp = 500.0
>
> gen_seed = 173529
>
> Please tell me why protein shows unfolding in very first frame.
>
> msnayeem
>
>
>
>
>
>
>
> On 4/7/10, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> >
> > On 7/04/2010 9:08 PM, shahid nayeem wrote:
> >
> >> Dear users
> >> Please let me know some basic question. I am sorry if I am asking a
> >> silly question.
> >> a) While simulating a protein thermal unfolding at high temperature say
> >> 500K should I run position restraint dynamics at 500k or at 298K. I am
> >> doing 100ps position restraint dynamics at 500k. Am I right in doing so.
> >>
> >
> > The usual purpose of position restrained MD is to allow the system to
> > achieve close to the ensemble desired for the start of the simulation
> > without perturbing the initial structure.
> >
> > b) While using Berendsen thermostat, how to select a value of tau_t and
> >> how does it affects simulation output. The same question for NoseHoover
> >> thermostat.
> >>
> >
> > Start by reading the GROMACS manual sections.
> >
> > c) After completing the 100ns simulation when I view the .xtc file in
> >> VMD I find that alpha helix of the protein is unfolded in very first
> >> frame collected at 10ps interval and reduced by trjconv at 50ps
> >> interval. Is it possible. If not then where I am wrong.
> >> I did Steepest descent minimization, then 100ps position restraint
> >> Dynamics at 500K and then 100ns full dynamics at 500k.
> >>
> >
> > 10ps would be very fast for a lengthy helix to unfold, however you've
> > deliberately taken your force field out of the zone where it was
> > parameterized, so we can't really infer anything about its behaviour. You
> > could also have a broken model physics in your .mdp file, but we can't
> know
> > about that.
> >
> > The real lesson here is not to do a lengthy simulation without looking at
> > the early and ongoing results.
> >
> > Mark
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> interface
> > or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
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> ------------------------------
>
> Message: 5
> Date: 8 Apr 2010 06:06:40 -0000
> From: "sarbani chattopadhyay" <sarbani_c84 at rediffmail.com>
> Subject: [gmx-users] Re:Re: g_nmeig_d error:cannot allocate region
> To: <gmx-users at gromacs.org>
> Message-ID: <20100408060640.59473.qmail at f5mail-236-240.rediffmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> I had checked and found that gromacs has been compiled in 64 bit mode.
> However still I am getting this error with "g_nmeig_d " command which says
> g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error
> code=12)
> *** error: can't allocate region
>
>
> I am running this on a 8 node machine,each with 2GB of RAM ( g_nmeig_d
> runs on a single node).
>
> Is it required to increase the RAM of 1 node to get rid of this error?
> Any suggestion will be very helpful.
> Thanking You,
> Sarbani
>
>
>
> On Tue, 02 Mar 2010 20:01:51 +0530 wrote
> >
> >
> >
> Hi,
> >
>
> >
> The allocation that causes the error should allocate about 3 GB.
> >
> My guess is that you compiled Gromacs in 32bit mode, whereas 64bit mode
> >
> is required for allocation of more than 2 GB.
> >
>
> >
> Berk
> >
>
> >
> Date: Tue, 2 Mar 2010 13:35:58 +0000
> >
> To: gmx-users at gromacs.org
> >
> From: sarbani_c84 at rediffmail.com
> >
> Subject: [gmx-users] g_nmeig_d error: can't allocate region
> >
>
> >
> Hi,
> >
>
> >
> I am trying to do normal mode analysis on a protein having 6398 atoms in
> vaccum.
>
> I tried to energy minimize the structure using steepest descent, followed
> by "l-bfgs"
> minimization. the .mdp file I used is
>
> define = -DFLEXIBLE
>
> constraints = none
> integrator = l-bfgs
> tinit = 0
> nsteps = 15000
> nbfgscorr = 50
> emtol = .001
> emstep = 0.1
> gen_vel = yes
> gen-temp = 300
> nstcomm = 1
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 0
> ; ns algorithm (simple or grid)
> ns-type = simple
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> or full (infinite systems only)
> pbc = no
> rlist = 0
> domain-decomposition = no
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = Cut-Off
> rcoulomb-switch = 0
> rcoulomb = 0
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch = 0
> rvdw = 0
>
> >
> after running the 15000 steps the Fmax was:>
> Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 10197 steps
>
> Potential Energy = -8.26391832320506e+04
>
> Maximum force = 9.37558560558845e-04 on atom 4562
>
> Norm of force = 2.24887722104890e-04
>
> Again the "l-bfgs" minimization was run using the same .mdp file( with
> emtol =
> 0.000001)>
> the output was'
> >
>
> >
> Low-Memory BFGS Minimizer converged to Fmax < 1e-06 in 4143 steps
> >
>
> >
> Potential Energy = -8.26391832324998e+04
> >
>
> >
> Maximum force = 9.67927896882578e-07 on atom 3271
> >
>
> >
> Norm of force = 1.70637151528245e-07
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
> After this I prepared the "nm.mdp " file for NMA, where I used exactly the
> same parameters
> >
>
> >
> as the ones used in lbfgs energy minimization( with integrator = nm)
> >
>
> >
>
> >
>
> >
> the commands that were used were:
> >
>
> >
> grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr
> -zero -p
> >
>
> >
> ../topol.top
> >
>
> >
>
> >
>
> >
> nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx &
> >
>
> >
>
> >
>
> >
>
> >
>
> >
> "nohup.out" had the following message:
> >
>
> >
> Non-cutoff electrostatics used, forcing full Hessian format.Allocating
> Hessian
> >
>
> >
> memory...starting normal mode calculation 'Protein'6398 steps.Maximum
> force: 9.67928e-07
> >
>
> >
>
> >
>
> >
>
> >
>
> >
> The run ended successfully:
> >
>
> >
>
> >
>
> >
> Then i used the command
> >
>
> >
> g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr
> >
>
> >
>
> >
>
> >
> I get the following error:
> >
>
> >
> Reading file new_nm.tpr, VERSION 4.0.7 (double precision)
> >
>
> >
> Reading file new_nm.tpr, VERSION 4.0.7 (double precision)
> >
>
> >
> Reading double precision matrix generated by Gromacs VERSION 4.0.7
> >
>
> >
> Full matrix storage format, nrow=19194, ncols=19194
> >
>
> >
>
> >
>
> >
> Diagonalizing to find vectors 1 through 50...
> >
>
> >
> g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error
> code=12)
> >
>
> >
> *** error: can't allocate region
> >
>
> >
> *** set a breakpoint in malloc_error_break to debug
> >
>
> >
>
> >
>
> >
> I am not being able to understand the problem. the computer has a 16gb
> memory
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
> If I use different parameters in the nm.mdp file as
> >
>
> >
>
> >
>
> >
> rlist = 1.5
> >
>
> >
> domain-decomposition = no
> >
>
> >
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >
>
> >
> ; Method for doing electrostatics
> >
>
> >
> coulombtype = switch
> >
>
> >
> rcoulomb-switch = 1
> >
>
> >
> rcoulomb = 1.2
> >
>
> >
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> >
>
> >
> epsilon-r = 1
> >
>
> >
> ; Method for doing Van der Waals
> >
>
> >
> vdw-type = switch
> >
>
> >
> ; cut-off lengths
> >
>
> >
> rvdw-switch = 1
> >
>
> >
> rvdw = 1.2
> >
>
> >
>
> >
>
> >
>
> >
>
> >
> then i get the message :Maximum force: 3.14171e+03
> >
>
> >
> Maximum force probably not small enough to ensure that you are in an
> >
>
> >
> energy well. Be aware that negative eigenvalues may occur when the
> >
>
> >
> resulting matrix is diagonalized.
> >
>
> >
>
> >
>
> >
>
> >
>
> >
> I am sorry to post such a lengthy query, but I have no clue about the root
> of the problem.
> >
>
> >
> Any suggestion will be of great help.
> >
>
> >
> Thanks in advance,
> >
>
> >
> Sarbani.
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 72, Issue 36
> *****************************************
>
--
Ozge Engin
★☆
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