Hi Ravi, <br><br>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.<br>
<br>Regards<br><br><div class="gmail_quote">On Thu, Apr 8, 2010 at 9:13 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br>
Today's Topics:<br>
<br>
1. RE: energy minimization in charged systems (Dallas B. Warren)<br>
2. Simulating a metal slab (radhika jaswal)<br>
3. Re: Simulating a metal slab (Mark Abraham)<br>
4. Re: position_restraint anfd full Dynamics and berendsen Nose<br>
hoover Thermostat (shahid nayeem)<br>
5. Re:Re: g_nmeig_d error:cannot allocate region<br>
(sarbani chattopadhyay)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 08 Apr 2010 15:22:53 +1000<br>
From: "Dallas B. Warren" <<a href="mailto:Dallas.Warren@pharm.monash.edu.au">Dallas.Warren@pharm.monash.edu.au</a>><br>
Subject: RE: [gmx-users] energy minimization in charged systems<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<89907EA1DCFB7548A431C13A270F9DD509B823C5@prk-exch-01.vcp.local><br>
Content-Type: text/plain; charset=iso-8859-1<br>
<br>
What are the atoms that are causing the problems actually doing, where are they located etc?<br>
<br>
Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Drug Delivery, Disposition and Dynamics<br>
Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@pharm.monash.edu.au">dallas.warren@pharm.monash.edu.au</a><br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.<br>
<br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of Ravi Bhadauria<br>
Sent: Thursday, 8 April 2010 3:11 PM<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] energy minimization in charged systems<br>
<br>
Hi all,<br>
<br>
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:<br>
<br>
t = 0.038 ps: Water molecule starting at atom 2569 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
and<br>
<br>
Steepest Descents converged to machine precision in 88 steps,<br>
but did not reach the requested Fmax < 1000.<br>
Potential Energy = 1.75456106043895e+06<br>
Maximum force = 1.07111309902475e+11 on atom 4898<br>
Norm of force = 1.48772609239112e+09<br>
<br>
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.<br>
<br>
Thanks in advance.<br>
<br>
--<br>
Ravi Bhadauria<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 8 Apr 2010 11:17:15 +0530 (IST)<br>
From: radhika jaswal <<a href="mailto:jaswalradhika@yahoo.co.in">jaswalradhika@yahoo.co.in</a>><br>
Subject: [gmx-users] Simulating a metal slab<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:109124.71315.qm@web94806.mail.in2.yahoo.com">109124.71315.qm@web94806.mail.in2.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hii Everybody...<br>
<br>
<br>
<br>
I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in<br>
length and 4-5 molecules wide just as to mimic a rigid metal slab for<br>
further interaction studies. Can gromacs library support this and how I<br>
can do that...<br>
<br>
All suggestions are welcome.<br>
<br>
<br>
<br>
Thanks<br>
<br>
<br>
<br>
Radhika<br>
<br>
<br>
<br>
Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! <a href="http://messenger.yahoo.com/download.php" target="_blank">http://messenger.yahoo.com/download.php</a><br>
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Message: 3<br>
Date: Thu, 08 Apr 2010 15:54:24 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Simulating a metal slab<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4BBD6F90.7080108@anu.edu.au">4BBD6F90.7080108@anu.edu.au</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
On 8/04/2010 3:47 PM, radhika jaswal wrote:<br>
> Hii Everybody...<br>
><br>
> I want to simulate a Titanium Oxide slab of approx. 8-9 molecules in<br>
> length and 4-5 molecules wide just as to mimic a rigid metal slab for<br>
> further interaction studies. Can gromacs library support this and how I<br>
> can do that...<br>
<br>
Yes, in principle. You will need a force field that supports such<br>
interactions, and GROMACS does not come with any. Your first place to<br>
look should be in the published literature for other simulations of such<br>
materials and such slabs. Don't assume GROMACS is the best tool for the<br>
task.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 8 Apr 2010 11:27:37 +0530<br>
From: shahid nayeem <<a href="mailto:msnayeem@gmail.com">msnayeem@gmail.com</a>><br>
Subject: Re: [gmx-users] position_restraint anfd full Dynamics and<br>
berendsen Nose hoover Thermostat<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:o2mea6f7fbe1004072257yedd75eebn7c8f2e714d14a6fc@mail.gmail.com">o2mea6f7fbe1004072257yedd75eebn7c8f2e714d14a6fc@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Please see the following pr.mdp and full.mdp<br>
pr.mdp<br>
<br>
<br>
cpp = /usr/bin/cpp<br>
<br>
define = -DPOSRES<br>
<br>
constraints = all-bonds<br>
<br>
integrator = md<br>
<br>
dt = 0.002 ; ps !<br>
<br>
nsteps = 50000 ; total 100 ps.<br>
<br>
nstcomm = 1<br>
<br>
nstxout = 500<br>
<br>
nstvout = 1000<br>
<br>
nstfout = 0<br>
<br>
nstlog = 10<br>
<br>
nstenergy = 10<br>
<br>
nstlist = 10<br>
<br>
ns_type = grid<br>
<br>
rlist = 1.0<br>
<br>
rcoulomb = 1.0<br>
<br>
rvdw = 1.0<br>
<br>
; Berendsen temperature coupling is on in two groups<br>
<br>
Tcoupl = berendsen<br>
<br>
tc-grps = Protein Non-protein<br>
<br>
tau_t = 0.1 0.1<br>
<br>
ref_t = 500 500<br>
<br>
; Energy monitoring<br>
<br>
energygrps = Protein Non-protein<br>
<br>
; Pressure coupling is not on<br>
<br>
Pcoupl = no<br>
<br>
tau_p = 0.5<br>
<br>
compressibility = 4.5e-5<br>
<br>
ref_p = 1.0<br>
<br>
; Generate velocites is on at 500 K.<br>
<br>
gen_vel = yes<br>
<br>
gen_temp = 500.0<br>
<br>
gen_seed = 173529<br>
<br>
full.mdp<br>
<br>
cpp = /usr/bin/cpp<br>
<br>
constraints = all-bonds<br>
<br>
integrator = md<br>
<br>
dt = 0.002 ; ps !<br>
<br>
nsteps = 50000000 ; total 100000 ps.<br>
<br>
nstcomm = 1<br>
<br>
nstxout = 5000<br>
<br>
nstvout = 40000<br>
<br>
nstfout = 0<br>
<br>
nstlog = 100<br>
<br>
nstenergy = 100<br>
<br>
nstlist = 10<br>
<br>
ns_type = grid<br>
<br>
rlist = 1.0<br>
<br>
rcoulomb = 1.0<br>
<br>
rvdw = 1.0<br>
<br>
; Berendsen temperature coupling is on in two groups<br>
<br>
Tcoupl = berendsen<br>
<br>
tc-grps = Protein Non-protein<br>
<br>
tau_t = 0.1 0.1<br>
<br>
ref_t = 500 500<br>
<br>
; Energy monitoring<br>
<br>
energygrps = Protein Non-protein<br>
<br>
; Isotropic pressure coupling is now on<br>
<br>
Pcoupl = berendsen<br>
<br>
Pcoupltype = isotropic<br>
<br>
tau_p = 0.5<br>
<br>
compressibility = 4.5e-5<br>
<br>
ref_p = 1.0<br>
<br>
; Generate velocites is off at 500 K.<br>
<br>
gen_vel = no<br>
<br>
gen_temp = 500.0<br>
<br>
gen_seed = 173529<br>
<br>
Please tell me why protein shows unfolding in very first frame.<br>
<br>
msnayeem<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 4/7/10, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>
><br>
> On 7/04/2010 9:08 PM, shahid nayeem wrote:<br>
><br>
>> Dear users<br>
>> Please let me know some basic question. I am sorry if I am asking a<br>
>> silly question.<br>
>> a) While simulating a protein thermal unfolding at high temperature say<br>
>> 500K should I run position restraint dynamics at 500k or at 298K. I am<br>
>> doing 100ps position restraint dynamics at 500k. Am I right in doing so.<br>
>><br>
><br>
> The usual purpose of position restrained MD is to allow the system to<br>
> achieve close to the ensemble desired for the start of the simulation<br>
> without perturbing the initial structure.<br>
><br>
> b) While using Berendsen thermostat, how to select a value of tau_t and<br>
>> how does it affects simulation output. The same question for NoseHoover<br>
>> thermostat.<br>
>><br>
><br>
> Start by reading the GROMACS manual sections.<br>
><br>
> c) After completing the 100ns simulation when I view the .xtc file in<br>
>> VMD I find that alpha helix of the protein is unfolded in very first<br>
>> frame collected at 10ps interval and reduced by trjconv at 50ps<br>
>> interval. Is it possible. If not then where I am wrong.<br>
>> I did Steepest descent minimization, then 100ps position restraint<br>
>> Dynamics at 500K and then 100ns full dynamics at 500k.<br>
>><br>
><br>
> 10ps would be very fast for a lengthy helix to unfold, however you've<br>
> deliberately taken your force field out of the zone where it was<br>
> parameterized, so we can't really infer anything about its behaviour. You<br>
> could also have a broken model physics in your .mdp file, but we can't know<br>
> about that.<br>
><br>
> The real lesson here is not to do a lengthy simulation without looking at<br>
> the early and ongoing results.<br>
><br>
> Mark<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www interface<br>
> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
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------------------------------<br>
<br>
Message: 5<br>
Date: 8 Apr 2010 06:06:40 -0000<br>
From: "sarbani chattopadhyay" <<a href="mailto:sarbani_c84@rediffmail.com">sarbani_c84@rediffmail.com</a>><br>
Subject: [gmx-users] Re:Re: g_nmeig_d error:cannot allocate region<br>
To: <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:20100408060640.59473.qmail@f5mail-236-240.rediffmail.com">20100408060640.59473.qmail@f5mail-236-240.rediffmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
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<br>
g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12)<br>
*** error: can't allocate region<br>
<br>
<br>
I am running this on a 8 node machine,each with 2GB of RAM ( g_nmeig_d runs on a single node).<br>
<br>
Is it required to increase the RAM of 1 node to get rid of this error?<br>
Any suggestion will be very helpful.<br>
Thanking You,<br>
Sarbani<br>
<br>
<br>
<br>
On Tue, 02 Mar 2010 20:01:51 +0530 wrote<br>
><br>
><br>
><br>
Hi,<br>
><br>
<br>
><br>
The allocation that causes the error should allocate about 3 GB.<br>
><br>
My guess is that you compiled Gromacs in 32bit mode, whereas 64bit mode<br>
><br>
is required for allocation of more than 2 GB.<br>
><br>
<br>
><br>
Berk<br>
><br>
<br>
><br>
Date: Tue, 2 Mar 2010 13:35:58 +0000<br>
><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
><br>
From: <a href="mailto:sarbani_c84@rediffmail.com">sarbani_c84@rediffmail.com</a><br>
><br>
Subject: [gmx-users] g_nmeig_d error: can't allocate region<br>
><br>
<br>
><br>
Hi,<br>
><br>
<br>
><br>
I am trying to do normal mode analysis on a protein having 6398 atoms in vaccum.<br>
<br>
I tried to energy minimize the structure using steepest descent, followed by "l-bfgs"<br>
minimization. the .mdp file I used is<br>
<br>
define = -DFLEXIBLE<br>
<br>
constraints = none<br>
integrator = l-bfgs<br>
tinit = 0<br>
nsteps = 15000<br>
nbfgscorr = 50<br>
emtol = .001<br>
emstep = 0.1<br>
gen_vel = yes<br>
gen-temp = 300<br>
nstcomm = 1<br>
; NEIGHBORSEARCHING PARAMETERS<br>
; nblist update frequency<br>
nstlist = 0<br>
; ns algorithm (simple or grid)<br>
ns-type = simple<br>
; Periodic boundary conditions: xyz (default), no (vacuum)<br>
or full (infinite systems only)<br>
pbc = no<br>
rlist = 0<br>
domain-decomposition = no<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
; Method for doing electrostatics<br>
coulombtype = Cut-Off<br>
rcoulomb-switch = 0<br>
rcoulomb = 0<br>
; Dielectric constant (DC) for cut-off or DC of reaction field<br>
epsilon-r = 1<br>
; Method for doing Van der Waals<br>
vdw-type = Cut-off<br>
; cut-off lengths<br>
rvdw-switch = 0<br>
rvdw = 0<br>
<br>
><br>
after running the 15000 steps the Fmax was:><br>
Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 10197 steps<br>
<br>
Potential Energy = -8.26391832320506e+04<br>
<br>
Maximum force = 9.37558560558845e-04 on atom 4562<br>
<br>
Norm of force = 2.24887722104890e-04<br>
<br>
Again the "l-bfgs" minimization was run using the same .mdp file( with emtol =<br>
0.000001)><br>
the output was'<br>
><br>
<br>
><br>
Low-Memory BFGS Minimizer converged to Fmax < 1e-06 in 4143 steps<br>
><br>
<br>
><br>
Potential Energy = -8.26391832324998e+04<br>
><br>
<br>
><br>
Maximum force = 9.67927896882578e-07 on atom 3271<br>
><br>
<br>
><br>
Norm of force = 1.70637151528245e-07<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
After this I prepared the "nm.mdp " file for NMA, where I used exactly the same parameters<br>
><br>
<br>
><br>
as the ones used in lbfgs energy minimization( with integrator = nm)<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
the commands that were used were:<br>
><br>
<br>
><br>
grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr -zero -p<br>
><br>
<br>
><br>
../topol.top<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx &<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
"nohup.out" had the following message:<br>
><br>
<br>
><br>
Non-cutoff electrostatics used, forcing full Hessian format.Allocating Hessian<br>
><br>
<br>
><br>
memory...starting normal mode calculation 'Protein'6398 steps.Maximum force: 9.67928e-07<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
The run ended successfully:<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
Then i used the command<br>
><br>
<br>
><br>
g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
I get the following error:<br>
><br>
<br>
><br>
Reading file new_nm.tpr, VERSION 4.0.7 (double precision)<br>
><br>
<br>
><br>
Reading file new_nm.tpr, VERSION 4.0.7 (double precision)<br>
><br>
<br>
><br>
Reading double precision matrix generated by Gromacs VERSION 4.0.7<br>
><br>
<br>
><br>
Full matrix storage format, nrow=19194, ncols=19194<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
Diagonalizing to find vectors 1 through 50...<br>
><br>
<br>
><br>
g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12)<br>
><br>
<br>
><br>
*** error: can't allocate region<br>
><br>
<br>
><br>
*** set a breakpoint in malloc_error_break to debug<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
I am not being able to understand the problem. the computer has a 16gb memory<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
If I use different parameters in the nm.mdp file as<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
rlist = 1.5<br>
><br>
<br>
><br>
domain-decomposition = no<br>
><br>
<br>
><br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
><br>
<br>
><br>
; Method for doing electrostatics<br>
><br>
<br>
><br>
coulombtype = switch<br>
><br>
<br>
><br>
rcoulomb-switch = 1<br>
><br>
<br>
><br>
rcoulomb = 1.2<br>
><br>
<br>
><br>
; Dielectric constant (DC) for cut-off or DC of reaction field<br>
><br>
<br>
><br>
epsilon-r = 1<br>
><br>
<br>
><br>
; Method for doing Van der Waals<br>
><br>
<br>
><br>
vdw-type = switch<br>
><br>
<br>
><br>
; cut-off lengths<br>
><br>
<br>
><br>
rvdw-switch = 1<br>
><br>
<br>
><br>
rvdw = 1.2<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
then i get the message :Maximum force: 3.14171e+03<br>
><br>
<br>
><br>
Maximum force probably not small enough to ensure that you are in an<br>
><br>
<br>
><br>
energy well. Be aware that negative eigenvalues may occur when the<br>
><br>
<br>
><br>
resulting matrix is diagonalized.<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
<br>
><br>
I am sorry to post such a lengthy query, but I have no clue about the root of the problem.<br>
><br>
<br>
><br>
Any suggestion will be of great help.<br>
><br>
<br>
><br>
Thanks in advance,<br>
><br>
<br>
><br>
Sarbani.<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Ozge Engin<br> ★☆<br>