[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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