[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
James Starlight
jmsstarlight at gmail.com
Fri Dec 7 17:42:37 CET 2012
Justin,
ligand-only simulation in vacuum have been finished with the same errors :)
Step 19200, time 38.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 52.2 0.1033 0.0985 0.1000
1 3 90.1 0.1168 0.1141 0.1000
Step 19200, time 38.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025376, max 0.140474 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 52.0 0.1033 0.0988 0.1000
1 3 90.0 0.1168 0.1140 0.1000
step 19200, will finish Sat Dec 8 04:10:49 2012
Step 19201, time 38.402 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052715, max 0.293316 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 49.3 0.0988 0.0993 0.1000
1 3 90.0 0.1140 0.1293 0.1000
Step 19201, time 38.402 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052900, max 0.294281 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 49.6 0.0988 0.0989 0.1000
1 3 90.0 0.1140 0.1294 0.1000
Step 19202, time 38.404 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035783, max 0.198482 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 33.3 0.0989 0.0984 0.1000
1 3 89.9 0.1294 0.1198 0.1000
-------------------------------------------------------
Program mdrun, VERSION 4.5.4
Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176
Fatal error:
Too many LINCS warnings (1000)
ITs intresting that the same files (like step-1c_n11.pdb) have been
produced already during CG minimisation phase but the system have not
been crashed. So I suppoe that the problem is in geometry of the
mollecule. The direct comparison of the bonds and angles with the rtp
(DGUA) is non trivial again because of differs in the file formats
representation :)
James
2012/12/7 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 12/7/12 10:41 AM, James Starlight wrote:
>>
>> Today I've tried to simulate complexes of my protein with the cyclic
>> GMP parametrized by ATB's. (below the recent parametrisation for
>> charges of that molecule done by am1 algorithm)
>>
>> [ moleculetype ]
>> ; Name nrexcl
>> _N4P 3
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass total_charge
>> 1 NT 1 _N4P N2 1 -0.848 14.0067
>> 2 H 1 _N4P H22 1 0.424 1.0080
>> 3 H 1 _N4P H21 1 0.424 1.0080 ; 0.000
>> 4 NR 1 _N4P N1 2 -0.684 14.0067
>> 5 H 1 _N4P H1 2 0.437 1.0080
>> 6 C 1 _N4P C2 2 0.779 12.0110
>> 7 NR 1 _N4P N3 2 -0.678 14.0067
>> 8 C 1 _N4P C4 2 0.440 12.0110
>> 9 NR 1 _N4P N9 2 -0.294 14.0067 ; 0.000
>> 10 C 1 _N4P C8 3 0.272 12.0110
>> 11 HC 1 _N4P H01 3 0.141 1.0080
>> 12 O 1 _N4P O6 3 -0.555 15.9994
>> 13 C 1 _N4P C6 3 0.608 12.0110
>> 14 C 1 _N4P C5 3 0.101 12.0110
>> 15 NR 1 _N4P N7 3 -0.567 14.0067 ; 0.000
>> 16 OE 1 _N4P O4* 4 -0.451 15.9994
>> 17 CH1 1 _N4P C1* 4 0.451 13.0190 ; 0.000
>> 18 OA 1 _N4P O5* 5 -0.394 15.9994
>> 19 P 1 _N4P PAQ 5 0.974 30.9738
>> 20 OM 1 _N4P OAR 5 -0.616 15.9994
>> 21 OA 1 _N4P O3* 5 -0.390 15.9994
>> 22 OA 1 _N4P OAS 5 -0.584 15.9994
>> 23 H 1 _N4P H03 5 0.491 1.0080
>> 24 CH2 1 _N4P C5* 5 0.281 14.0270
>> 25 CH1 1 _N4P C4* 5 0.238 13.0190 ; 0.000
>> 26 CH1 1 _N4P C3* 6 0.000 13.0190 ; 0.000
>> 27 CH1 1 _N4P C2* 7 0.181 13.0190
>> 28 OA 1 _N4P O2* 7 -0.645 15.9994
>> 29 H 1 _N4P H8M 7 0.464 1.0080 ; 0.000
>>
>> In all cases my system have always been crushed after equilibration
>> run ( during that phase with the posres applied on both protein as
>> well as ligand the system was stabile) with the errors like
>>
>> Step 19, time 0.038 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 1.203662, max 11.750027 (between atoms 4289 and 4287)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 4288 4287 89.5 0.2277 1.1291 0.1000
>> 4292 4287 90.5 0.1304 0.9898 0.1350
>> 4289 4287 90.4 0.1056 1.2750 0.1000
>> 4318 4303 30.8 0.1531 0.1816 0.1530
>> 4304 4303 45.2 0.1097 0.1531 0.1090
>> 4309 4310 90.0 0.2629 0.3419 0.1000
>> 4299 4290 84.2 0.1404 0.1641 0.1400
>> 4292 4290 89.4 0.1362 0.5025 0.1380
>> 4291 4290 89.2 0.1563 0.2142 0.1000
>> 4293 4292 89.1 0.1252 0.5682 0.1320
>> 4294 4293 78.1 0.1387 0.3906 0.1350
>> 4300 4294 92.2 0.1385 0.4639 0.1390
>> 4295 4294 91.1 0.1365 0.5711 0.1380
>> 4303 4295 43.4 0.1482 0.1954 0.1470
>> 4296 4295 36.6 0.1408 0.1593 0.1400
>> 4301 4296 89.9 0.1323 0.5162 0.1320
>> 4297 4296 32.5 0.1089 0.1343 0.1090
>> 4299 4298 87.0 0.1230 0.2758 0.1230
>> 4300 4299 89.8 0.1431 0.5922 0.1430
>> 4301 4300 79.0 0.1381 0.1928 0.1380
>>
>>
>> Fatal error:
>> 1 particles communicated to PME node 26 are more than 2/3 times the
>> cut-off out of the domain decomposition cell of their charge group in
>> dimension y.
>> This usually means that your system is not well equilibrated.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>
>> After that my system have been crashed and than produced many
>> step*.pdb files in the work dirr.
>>
>> It's intresting that with the prodrg topology of that mollecule ( with
>> worst charge distribution) I've never such problems. Might that error
>> be due to the wrong geometry parametrisation (e.g incorect dihedrals)
>> of the cGMP made by ATB ?
>>
>
> Simulate all components of your system separately and follow
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System.
> Dihedrals should not be a major issue, since all of them can be adequately
> described by those already present in the parent force field. Check against
> DGUA.
>
>
> -Justin
>
> --
> ========================================
>
> 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
>
> ========================================
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