<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
</head>
<body text="#000000" bgcolor="#ffffff">
<div class="moz-text-html" lang="x-western">
<div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 14px;" lang="x-western">Hi all, <br>
<br>
I'm trying to run implicit solvent calculations in gromacs 4.5
with the charmm forcefield. I am able to minimize successfully
and compile for mdrun, but soon after starting, mdrun complains
about excessive rotation in LINCS (see the error printed below
that). I also include my mdp file at the bottom. Can anyone
advise me as to the possible cause of such errors, as it is
difficult to diagnose given that grompp worked fine. <br>
<br>
--- lincs error --- <br>
<br>
Step 1, time 0.002 (ps) LINCS WARNING <br>
relative constraint deviation after LINCS: <br>
rms 0.000780, max 0.020692 (between atoms 880 and 881) <br>
bonds that rotated more than 30 degrees: <br>
atom 1 atom 2 angle previous, current, constraint length <br>
606 607 36.7 1.0527 0.1080 0.1080 <br>
614 615 35.6 0.8972 0.1125 0.1111 <br>
614 616 75.3 0.1054 0.1121 0.1111 <br>
880 881 58.0 0.1068 0.1134 0.1111 <br>
880 882 50.4 0.9168 0.1121 0.1111 <br>
889 890 55.3 0.1066 0.1122 0.1111 <br>
889 891 35.3 0.8588 0.1118 0.1111 <br>
<br>
---- mdp file ------------ <br>
<br>
; title and include files <br>
title = 1EX6-S35P_md1 <br>
cpp = cpp <br>
include =
-I/home/yoo2/myusr/gromacs-3.3.3/share/gromacs/top/ -I./ <br>
define = <br>
; integrator and input/output setting up <br>
integrator = md <br>
nsteps = 1000000 ; 2 ns <br>
;nsteps = 5000 ; 2 ns <br>
dt = 0.002 <br>
nstxout = 5000 <br>
nstvout = 5000 <br>
nstenergy = 500 <br>
nstxtcout = 500 <br>
nstlog = 500 <br>
xtc_grps = System <br>
energygrps = System <br>
comm_mode = Linear <br>
<br>
;implicit solvent <br>
implicit_solvent = GBSA <br>
gb_algorithm = Still <br>
gb_saltconc = 0.15 <br>
rgbradii = 1.0 <br>
<br>
; neighbor searching and vdw/pme setting up <br>
nstlist = 10 <br>
ns_type = grid <br>
pbc = xyz <br>
;rlist = 1.4 <br>
rlist = 1.0 <br>
<br>
;coulombtype = pme <br>
coulombtype = Cut-Off <br>
fourierspacing = 0.1 <br>
pme_order = 6 <br>
;rcoulomb = 1.4 <br>
rcoulomb = 1.1 <br>
<br>
;vdwtype = switch <br>
vdwtype = Cut-Off <br>
rvdw_switch = 1.0 <br>
;rvdw = 1.2 <br>
rvdw = 1.1 <br>
<br>
; cpt control <br>
tcoupl = nose-hoover <br>
tc-grps = System <br>
tau_t = 0.4 <br>
ref_t = 300.0 <br>
Pcoupl = parrinello-rahman <br>
pcoupltype = isotropic <br>
tau_p = 1.0 <br>
compressibility = 4.5e-5 <br>
ref_p = 1.0 <br>
<br>
; velocity & temperature control <br>
gen_vel = yes <br>
gen_temp = 300.0 <br>
annealing = no <br>
constraints = hbonds <br>
;constraints = none <br>
constraint_algorithm = lincs <br>
;constraint_algorithm = shake <br>
morse = no <br>
<br>
Mike <br>
<br>
<div class="moz-txt-sig"><span class="moz-txt-tag">-- <br>
</span>Michael D. Daily, Ph.D. <br>
Postdoctoral Fellow <br>
Qiang Cui group <br>
Department of Chemistry <br>
University of Wisconsin-Madison <br>
<br>
</div>
</div>
<br>
<pre class="moz-signature" cols="72">--
Michael D. Daily, Ph.D.
Postdoctoral Fellow
Qiang Cui group
Department of Chemistry
University of Wisconsin-Madison
</pre>
</div>
<br>
<pre class="moz-signature" cols="72">--
Michael D. Daily, Ph.D.
Postdoctoral Fellow
Qiang Cui group
Department of Chemistry
University of Wisconsin-Madison
</pre>
</body>
</html>