[gmx-users] Re: A note while running grompp for nvt equilibration
Emanuel Birru
Emanuel.Birru at monash.edu
Thu Feb 21 05:53:41 CET 2013
There might be more than one reason for this kind of error.
1. check your topology file specially for the 1-4 interaction error.
2. check your coordinate file (gro/pdb file), weather it is correct or not.
3. do the minimization for more steps than you did before.
4. check which atoms are making the LINCS warning (for eg. 24349 24347).
5. if they hare hydrogen atoms make them heavy.
6. if that doesn't help increase your time step.
If you describe your system well and give us a chance to see you top and mdp files it would be easy to address the problem directly.
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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