[gmx-users] ERROR: pressure coupling not enough values (I need 1)
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 12 13:20:07 CEST 2009
Ms. Aswathy S wrote:
> I have specified ref_p as 1, now grommp works fine.but show the error as below. From the previous post what I understood is this is a problem with the gromacs version. I am using Gromacs3.2.1. Is that could be the problem??
>
Well, there certainly have been improvements to the code since version 3.2.1,
which is over 5 years old, but the version is not causing the problem.
Your system is blowing because something is unstable. See here:
http://oldwiki.gromacs.org/index.php/blowing_up
http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
-Justin
> Back Off! I just backed up minim+ener.edr to ./#minim+ener.edr.2#
> starting mdrun 'Protein in water'
> 10000 steps, 20.0 ps.
>
>
> Back Off! I just backed up RBP4_em_eq1_20ps.trr to ./#RBP4_em_eq1_20ps.trr.2#
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 1428.842651 (between atoms 1547 and 1548) rms 43.118099
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 50 51 93.1 0.1530 1.1319 0.1530
> 51 52 92.8 0.1470 4.0768 0.1470
> 52 53 95.0 0.1000 3.3258 0.1000
> 52 54 93.7 0.1340 9.4062 0.1340
> 54 55 93.2 0.1340 8.3665 0.1340
> 54 58 90.5 0.1340 47.1335 0.1340
> 55 56 91.6 0.1000 4.4466 0.1000
> 55 57 91.5 0.1000 4.4648 0.1000
> 58 59 90.2 0.1000 48.3157 0.1000
> 58 60 90.2 0.1000 47.7912 0.1000
> 74 75 90.0 0.1430 0.9637 0.1430
> 75 76 90.0 0.1000 0.3743 0.1000
> 112 116 30.3 0.1340 0.1354 0.1340
> 116 117 36.7 0.1000 0.1036 0.1000
> 116 118 52.9 0.1000 0.1068 0.1000
> 156 158 88.6 0.1330 0.1471 0.1330
> 158 159 89.5 0.1000 0.1658 0.1000
> 158 160 89.4 0.1000 0.1357 0.1000
> 314 315 90.0 0.1780 0.3872 0.1780
> 474 475 94.7 0.1530 0.0262 0.1530
> 475 476 91.5 0.1530 0.3873 0.1530
> 476 477 90.5 0.1250 0.7752 0.1250
> 476 478 91.9 0.1250 0.3319 0.1250
> 677 678 93.2 0.1530 0.3123 0.1530
> 678 679 92.8 0.1530 0.9707 0.1530
> 679 680 92.4 0.1230 0.9836 0.1230
> 679 681 90.6 0.1330 3.5962 0.1330
> 681 682 90.2 0.1000 3.8687 0.1000
> 681 683 90.2 0.1000 3.6579 0.1000
> 1200 1204 36.1 0.1390 0.1420 0.1390
> 1204 1205 90.0 0.1080 1.8158 0.1080
> 1204 1206 33.9 0.1390 0.1433 0.1390
> 1542 1544 98.5 0.1470 0.6632 0.1470
> 1544 1545 94.3 0.1530 5.8372 0.1530
> 1544 1552 98.5 0.1530 0.6695 0.1530
> 1545 1546 91.3 0.1530 39.3403 0.1530
> 1546 1547 93.3 0.1530 69.5871 0.1530
> 1547 1548 91.1 0.1230 175.8707 0.1230
> 1547 1549 93.2 0.1330 71.3069 0.1330
> 1549 1550 91.5 0.1000 39.8680 0.1000
> 1549 1551 91.4 0.1000 40.0342 0.1000
> 1625 1626 38.0 0.1000 0.1028 0.1000
> 1625 1627 32.7 0.1000 0.1012 0.1000
> 1715 1717 39.9 0.1330 0.1337 0.1330
> 1717 1718 64.0 0.1000 0.1027 0.1000
> 1717 1719 63.0 0.1000 0.1019 0.1000
>
> Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2#
>
> Back Off! I just backed up step0.pdb to ./#step0.pdb.2#
> Wrote pdb files with previous and current coordinates
> step 0
> MPI process rank 0 (n0, p9393) caught a SIGSEGV.
>
>
> Thanks,
> Aswathy
>
>
> Dept. Biotechnology
> Ext. 3108
>
> ----- Original Message -----
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Friday, June 12, 2009 4:31:28 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
> Subject: Re: [gmx-users] ERROR: pressure coupling not enough values (I need 1)
>
>
>
> Ms. Aswathy S wrote:
>> Hi,
>>
>> thanks for the help till now..
>>
>> Now I got a problem that an equilibration step of 20 ps shows an error as follows when i run grommp.
>>
>> ERROR: pressure coupling not enough values (I need 1)
>>
>> Please find the md.mdp file that I have used for this step.
>>
>
> You haven't specified ref_p.
>
> -Justin
>
>> thanks,
>> Aswathy
>> Dept. Biotechnology
>> Ext. 3108
>>
>>
>> ------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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