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??
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" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@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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