the same mdp file does the equlibriation fine at dt =0.0002 rather than 0.002.what could be the problem.if so can i continue using 0.0002 for dt in this simulation.Anad also the cnt is not infinite adn also the graphen sheets are not infinite.<br>
<br><div class="gmail_quote">On Sat, Jun 11, 2011 at 4:52 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
sreelakshmi ramesh wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
<br>
---------- Forwarded message ----------<br>
From: *sreelakshmi ramesh* <<a href="mailto:sree.lakshmi@research.iiit.ac.in" target="_blank">sree.lakshmi@research.iiit.ac.in</a> <mailto:<a href="mailto:sree.lakshmi@research.iiit.ac.in" target="_blank">sree.lakshmi@research.iiit.ac.in</a>>><br>
Date: Sat, Jun 11, 2011 at 4:37 PM<br>
Subject: Re: error during equilibriation<br></div><div class="im">
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<br>
<br>
here goes my mdp file.The when i attach the top file by mail is getting bounced back.Thanks in adcvance <br>
<br>
<br>
<br>
title = double walled cnt between graphene sheets<br>
</div></blockquote>
<br>
Is the CNT and/or the graphene infinite? If any species are, then you need to use the periodic_molecules keyword.<br>
<br>
How successful was energy minimization? What was the output (Fmax and Epot)?<br>
<br>
I see nothing particularly wrong with the .mdp file (other than perhaps the keyword mentioned above), so that suggests either the topology or the initial configuration is not sound.<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
define = -DPOSRES ; position restrain the protein<br>
; Run parameters<br>
<br>
integrator = md ; leap-frog integrator<br>
nsteps = 50000 ; 2 * 50000 = 100 ps<br>
dt = 0.002 ; 2 fs<br>
; Output control<br>
nstxout = 100 ; save coordinates every 0.2 ps<br>
nstvout = 100 ; save velocities every 0.2 ps<br>
<br>
<br>
nstenergy = 100 ; save energies every 0.2 ps<br>
nstlog = 100 ; update log file every 0.2 ps<br>
; Bond parameters<br>
continuation = no ; first dynamics run<br>
constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>
<br>
<br>
lincs_iter = 1 ; accuracy of LINCS<br>
lincs_order = 4 ; also related to accuracy<br>
; Neighborsearching<br>
ns_type = grid ; search neighboring grid cells<br>
nstlist = 5 ; 10 fs<br>
rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>
<br>
<br>
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>
; Electrostatics<br>
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>
pme_order = 4 ; cubic interpolation<br>
<br>
<br>
fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen thermostat<br>
tc-grps = system ; two coupling groups - more accurate<br>
tau_t = 0.1 ; time constant, in ps<br>
<br>
<br>
ref_t = 300 ; reference temperature, one for each group, in K<br>
; Pressure coupling is off<br>
pcoupl = no ; no pressure coupling in NVT<br>
; Periodic boundary conditions<br>
pbc = xyz ; 3-D PBC<br>
; Dispersion correction<br>
<br>
<br>
DispCorr = EnerPres ; account for cut-off vdW scheme<br>
; Velocity generation<br>
gen_vel = yes ; assign velocities from Maxwell distribution<br>
gen_temp = 300 ; temperature for Maxwell distribution<br>
gen_seed = -1 ; generate a random seed<br>
<br>
<br>
<br>
<br>
here goes the error<br>
Not all bonded interactions have been properly assigned to the domain decomposition cells<br>
<br>
<br>
A list of missing interactions:<br>
Angle of 2097 missing 14<br>
Ryckaert-Bell. of 1286 missing 12<br>
LJ-14 of 2801 missing 8<br>
exclusions of 31870 missing 14<br>
<br>
Molecule type 'ICE'<br>
the first 10 missing interactions, except for exclusions:<br>
LJ-14 atoms 79 299 global 79 299<br>
LJ-14 atoms 165 299 global 165 299<br>
Angle atoms 167 207 299 global 167 207 299<br>
Ryckaert-Bell. atoms 167 207 299 285 global 167 207 299 285<br>
Ryckaert-Bell. atoms 173 175 285 299 global 173 175 285 299<br>
LJ-14 atoms 173 299 global 173 299<br>
LJ-14 atoms 173 352 global 173 352<br>
Angle atoms 175 285 299 global 175 285 299<br>
Angle atoms 175 285 352 global 175 285 352<br>
Ryckaert-Bell. atoms 175 285 299 207 global 175 285 299 207<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.3<br>
Source code file: domdec_top.c, line: 356<br>
<br>
Fatal error:<br>
48 of the 46602 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
<br>
<br>
</blockquote>
<br></div></div><div><div></div><div class="h5">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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