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Hi,<br><br>The allocation that causes the error should allocate about 3 GB.<br>My guess is that you compiled Gromacs in 32bit mode, whereas 64bit mode<br>is required for allocation of more than 2 GB.<br><br>Berk<br><br><hr id="stopSpelling">Date: Tue, 2 Mar 2010 13:35:58 +0000<br>To: gmx-users@gromacs.org<br>From: sarbani_c84@rediffmail.com<br>Subject: [gmx-users] g_nmeig_d error: can't allocate region<br><br>Hi,<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>
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>
; nblist cut-off<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>
Potential Energy = -8.26391832320506e+04<br>
Maximum force = 9.37558560558845e-04 on atom 4562<br>
Norm of force = 2.24887722104890e-04<br>
<br>
<br>
Again the "l-bfgs" minimization was run using the same .mdp file( with emtol = 0.000001)<br>
<br>
the output was'<br>
Low-Memory BFGS Minimizer converged to Fmax < 1e-06 in 4143 steps<br>
Potential Energy = -8.26391832324998e+04<br>
Maximum force = 9.67927896882578e-07 on atom 3271<br>
Norm of force = 1.70637151528245e-07<br>
<br>
<br>
<br>
After this I prepared the "nm.mdp " file for NMA, where I used exactly the same parameters <br>
as the ones used in lbfgs energy minimization( with integrator = nm)<br>
<br>
the commands that were used were:<br>
grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr -zero -p <br>
../topol.top<br>
<br>
nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx &<br>
<br>
<br>
"nohup.out" had the following message:<br>
Non-cutoff electrostatics used, forcing full Hessian format.Allocating Hessian <br>
memory...starting normal mode calculation 'Protein'6398 steps.Maximum force: 9.67928e-<br>
07<br>
<br>
<br>
The run ended successfully:<br>
<br>
Then i used the command <br>
g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr<br>
<br>
I get the following error:<br>
Reading file new_nm.tpr, VERSION 4.0.7 (double precision)<br>
Reading file new_nm.tpr, VERSION 4.0.7 (double precision)<br>
Reading double precision matrix generated by Gromacs VERSION 4.0.7<br>
Full matrix storage format, nrow=19194, ncols=19194<br>
<br>
Diagonalizing to find vectors 1 through 50...<br>
g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12)<br>
*** error: can't allocate region<br>
*** set a breakpoint in malloc_error_break to debug<br>
<br>
I am not being able to understand the problem. the computer has a 16gb memory<br>
<br>
<br>
<br>
If I use different parameters in the nm.mdp file as<br>
<br>
rlist = 1.5<br>
domain-decomposition = no<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
; Method for doing electrostatics<br>
coulombtype = switch<br>
rcoulomb-switch = 1<br>
rcoulomb = 1.2<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 = switch<br>
; cut-off lengths<br>
rvdw-switch = 1<br>
rvdw = 1.2<br>
<br>
<br>
then i get the message :Maximum force: 3.14171e+03<br>
Maximum force probably not small enough to ensure that you are in an<br>
energy well. Be aware that negative eigenvalues may occur when the<br>
resulting matrix is diagonalized.<br>
<br>
<br>
I am sorry to post such a lengthy query, but I have no clue about the root of the problem.<br>
Any suggestion will be of great help.<br>
Thanks in advance,<br>
Sarbani. <br><table style="font-family: Verdana; font-size: 11px; line-height: 15px;" width="644" border="0" cellpadding="0" cellspacing="0" height="57"><tbody><tr><td><a href="http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?"><img src="http://sigads.rediff.com/RealMedia/ads/adstream_nx.ads/www.rediffmail.com/signatureline.htm@Middle"></a></td></tr></tbody></table> <br /><hr />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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