[gmx-users] Re: A note while running grompp for nvt equilibration
Anu Chandran
miscofanu at gmail.com
Fri Feb 22 05:38:17 CET 2013
Thanks a lot of suggestions. Now my simulation is running without any
errors.
I have decreased the box dimension (by using -d 1.2 in editconf) and also
by using cutoff with
rlist=rvdw=rcoulomb=1.0. Now there is no warning or errors in nvt and npt
equilibration.
Thank you,
with regards,
Anu
On Thu, Feb 21, 2013 at 10:32 AM, Emanuel Birru <Emanuel.Birru at monash.edu>wrote:
>
> Correction on #6
> 6. if that doesn't help decrease your time step.
> Sorry for the confusion :)
>
> Cheers,
> EB
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Anu Chandran
> Sent: Thursday, 21 February 2013 3:34 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Re: A note while running grompp for nvt
> equilibration
>
> Sir,
> I tried using cutoff for van der Waals interactions. I got the following
> error during the nvt equilibration:
>
>
> "step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.040332, max 2.236585 (between atoms 24073 and 24072) bonds that
> rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length Wrote pdb
> files with previous and current coordinates
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.005594, max 0.252567 (between atoms 24347 and 24344) bonds that
> rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 24349 24347 34.7 0.1517 0.1322 0.1250
> 24383 24381 39.0 0.2108 0.1438 0.1340
> 24382 24381 31.8 0.1027 0.1089 0.1010
> 24387 24383 32.0 0.2041 0.1399 0.1340
> 24388 24387 30.3 0.2493 0.1070 0.1010
> 24344 24342 54.8 0.2383 0.1843 0.1529
> 24347 24344 49.3 0.2560 0.1906 0.1522
> 24346 24344 50.0 0.2082 0.1295 0.1090
> 24345 24344 56.2 0.1728 0.1357 0.1090
> 24063 24061 34.7 0.2181 0.1461 0.1335
> 24072 24063 39.2 0.1828 0.1480 0.1449
> starting mdrun 'Protein in water'
> 50000 steps, 100.0 ps.
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 9.003327, max 419.005005 (between atoms 24380 and 24378) bonds that
> rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 24381 24378 97.3 0.1825 59.6595 0.1463
> 24380 24378 122.0 0.1260 45.7805 0.1090
> 24379 24378 111.1 0.1319 28.6967 0.1090
> 24073 24072 90.2 0.3528 0.8138 0.1090
> 24349 24347 89.7 0.1517 46.2536 0.1250
> 24348 24347 95.7 0.1756 13.5872 0.1250
> 24383 24381 86.4 0.2108 5.1830 0.1340
> 24382 24381 105.2 0.1027 2.7271 0.1010
> 24387 24383 85.2 0.2041 2.1027 0.1340
> 24384 24383 88.3 0.0874 2.5321 0.1340
> 24386 24384 92.8 0.1068 3.6505 0.1010
> 24385 24384 88.0 0.0997 3.7036 0.1010
> 24389 24387 88.7 0.2448 1.5454 0.1010
> 24388 24387 88.4 0.2493 1.5186 0.1010
> 24368 24366 74.3 0.1338 0.2409 0.1335
> 24367 24366 104.8 0.1231 0.0883 0.1229
> 24370 24368 103.0 0.1458 5.0355 0.1449
> 24369 24368 96.3 0.1012 0.2541 0.1010
> 24390 24370 121.9 0.1532 4.8700 0.1522
> 24371 24370 97.9 0.1097 5.0227 0.1090
> 24375 24372 80.9 0.1936 9.2201 0.1529
> 24374 24372 92.0 0.1124 1.9509 0.1090
> 24373 24372 86.1 0.1124 1.8518 0.1090
> 24378 24375 99.7 0.1500 49.8084 0.1529
> 24377 24375 86.5 0.1471 16.9457 0.1090
> 24376 24375 87.1 0.1476 15.3512 0.1090
> 24392 24390 71.6 0.1338 0.2163 0.1335
> 24391 24390 72.8 0.1231 0.3302 0.1229
> 24394 24392 152.1 0.1450 0.1137 0.1449
> 24393 24392 121.6 0.1011 0.1883 0.1010
> 24414 24394 32.9 0.1523 0.1900 0.1522
> 24396 24394 33.8 0.1529 0.1910 0.1529
> 24395 24394 40.7 0.1090 0.1519 0.1090
> 24342 24340 133.3 0.1870 0.5324 0.1449
> 24350 24342 80.5 0.1906 0.6983 0.1522
> 24344 24342 85.5 0.2383 4.0017 0.1529
> 24343 24342 90.9 0.1423 0.6476 0.1090
> 24347 24344 104.1 0.2560 11.9267 0.1522
> 24346 24344 81.7 0.2082 3.4103 0.1090
> 24345 24344 82.9 0.1728 4.6679 0.1090
> 24354 24352 38.4 0.1465 0.1761 0.1449
> 24366 24354 54.4 0.1527 0.0985 0.1522
> 24063 24061 31.1 0.2181 0.1464 0.1335
> 24072 24063 30.6 0.1828 0.1463 0.1449
> 24068 24066 46.3 0.1202 0.1123 0.1090
> 24067 24066 44.6 0.1209 0.1131 0.1090
> 24070 24069 92.8 0.0417 0.1386 0.1090
>
> step 0: Water molecule starting at atom 395505 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> wrote pdb files with previous and current coordinates step 0
> Warning: 1-4 interaction between 24378 and 24384 at distance 61.758 which
> is larger than the 1-4 table size 2.000 nm These are ignored for the rest
> of the simulation This usually means your system is exploding, if not, you
> should increase table-extension in your mdp file or with user tables
> increase the table size
> ------------------------------------------------------
> Program mdrun, VERSION 4.5.3
> Source code file: pme.c, line: 534
>
> Fatal error:
> 5 particles communicated to PME node 2 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated."
>
>
> Thank You,
>
> regards,
> Anu
>
>
>
>
> On Tue, Feb 19, 2013 at 6:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 2/19/13 1:36 AM, Anu Chandran wrote:
> >
> >> Sir,
> >> Thank you for the reply. As per the suggestion, I tried increasing
> >> the rlist. Note or warning stopped when rlist was increased to 1.8.
> >> Also with this value of rcoulomb, the box size also needs to be
> >> increased. I would like to know whether it is fine to keep rlist 1.8
> >> and also whether there is any other alternative rather than
> >> increasing rlist since increase in rlist requires an increase in box
> >> size.
> >>
> >
> > I would investigate why you have such large charge groups. For a
> > protein in water (which is what you appear to have based on the .mdp
> > file), you should not have such large charge groups. Haphazardly
> > adjusting cutoffs can have a negative effect on the simulation.
> > Increasing rlist may result in poorer performance. Why are you using
> > a switching potential for van der Waals interactions? Exact
> > specifications for OPLS are hard to come by in the literature, but most
> commonly one sees:
> >
> > rvdw = 1.0
> > vdwtype = cutoff
> > rlist = 1.0
> > rcoulomb = 1.0
> > coulombtype = PME
> >
> > -Justin
> >
> >
> > Thank you,
> >> with regards
> >> Anu
> >>
> >> On Fri, Feb 15, 2013 at 5:28 PM, Dr. Vitaly Chaban
> >> <vvchaban at gmail.com
> >> >wrote:
> >>
> >> I am tyring to do a simulation of a monomer and an octamer of the
> >> same
> >>>> molecule
> >>>> using gromacs 4.5.3 with opls force field. Monomer simulations ran
> >>>> with
> >>>>
> >>> out
> >>>
> >>>> any note or
> >>>> warning, but when i tried to do nvt equilibration for the octamer,
> >>>> i got
> >>>>
> >>> the
> >>>
> >>>> following note while running grompp
> >>>>
> >>>> "NOTE 1 [file nvt.mdp]:
> >>>> The sum of the two largest charge group radii (0.779095) is
> >>>> larger than
> >>>> rlist (1.400000) - rvdw (1.000000)"
> >>>> The mdp file used is as follows:
> >>>>
> >>>> define = -DPOSRES
> >>>> integrator = md
> >>>> dt = 0.002
> >>>> nsteps = 50000
> >>>> nstcomm = 10
> >>>> nstxout = 100
> >>>> nstvout = 100
> >>>> nstlog = 100
> >>>> nstenergy = 100
> >>>> nstlist = 5
> >>>> ns_type = grid
> >>>> pbc = xyz
> >>>> rlist = 1.4
> >>>> coulombtype = PME
> >>>> rcoulomb = 1.4
> >>>> epsilon_r = 1
> >>>> vdwtype = Switch
> >>>> rvdw_switch = 0.9
> >>>> rvdw = 1.00
> >>>> fourierspacing = 0.12
> >>>> pme_order = 4
> >>>> ewald_rtol = 1e-5
> >>>> optimize_fft = yes
> >>>> Tcoupl = nose_hoover
> >>>> tc_grps = Protein Non-Protein
> >>>> tau_t = 0.4 0.4
> >>>> ref_t = 300 300
> >>>> nh-chain-length = 1
> >>>> pcoupl = no
> >>>> gen_vel = yes
> >>>> gen_temp = 300.0
> >>>> gen_seed = 1984
> >>>> continuation = no
> >>>> constraints = all-bonds
> >>>> constraint-algorithm = LINCS
> >>>> lincs-order = 4
> >>>> lincs-iter = 1
> >>>> lincs-warnangle = 30
> >>>>
> >>>>
> >>>> Can anybody please help me on how to go about with it?
> >>>>
> >>>
> >>>
> >>> 1) Increase RLIST
> >>> 2) Re-distribute atoms among charge groups so that to make charge
> >>> groups [spatially] smaller.
> >>>
> >>>
> >>>
> >>> Dr. Vitaly V. Chaban
> >>> MEMPHYS - Center for Biomembrane Physics Department of Physics,
> >>> Chemistry and Pharmacy University of Southern Denmark Campusvej 55,
> >>> 5230 Odense M, Denmark
> >>> --
> >>> gmx-users mailing list gmx-users at gromacs.org
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> >>>
> > --
> > ==============================**==========
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.
> > bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==============================**==========
> >
> > --
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