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On 17/03/2012 7:29 PM, Wholly Peach wrote:
<blockquote
cite="mid:1331972974.75168.YahooMailNeo@web121302.mail.ne1.yahoo.com"
type="cite">
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<div><span>Dear All,</span></div>
<div><span></span> </div>
<div><span>Will you please tell me the newest version of GROMACS
that can be installed under Cygwin?</span></div>
</div>
</blockquote>
<br>
4.5.5, per <a
href="http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO">http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO</a><br>
<br>
Your problems during make after correct configuration are probably
related to <a
href="http://x.cygwin.com/docs/faq/cygwin-x-faq.html#q-fork-failures">http://x.cygwin.com/docs/faq/cygwin-x-faq.html#q-fork-failures</a>,
and will be transient, as I have suggested to you before.<br>
<br>
Mark<br>
<br>
<a
href="http://x.cygwin.com/docs/faq/cygwin-x-faq.html#q-fork-failures"></a>
<blockquote
cite="mid:1331972974.75168.YahooMailNeo@web121302.mail.ne1.yahoo.com"
type="cite">
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New, courier, monaco, monospace, sans-serif;font-size:12pt">
<div><span></span> </div>
<div><span>I have tried, the elder version (3.3.1 version)can be
installed under cygvin sucessfully under cygvin, but the
4.5.5 and 4.5.4 version could not.</span></div>
<div><span></span> </div>
<div><span>I am looking forward to getting a reply from you on
it.</span></div>
<div><span></span> </div>
<div><span>Cheers,</span></div>
<div><span></span> </div>
<div><span>Wholly</span></div>
<div><br>
</div>
<div style="font-family: Courier New, courier, monaco,
monospace, sans-serif; font-size: 12pt;">
<div style="font-family: times new roman, new york, times,
serif; font-size: 12pt;">
<div dir="ltr"> <font face="Arial" size="2"> <b><span
style="font-weight: bold;">From:</span></b> Tsjerk
Wassenaar <a class="moz-txt-link-rfc2396E" href="mailto:tsjerkw@gmail.com"><tsjerkw@gmail.com></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Wholly Peach <a class="moz-txt-link-rfc2396E" href="mailto:whollypeach@yahoo.com"><whollypeach@yahoo.com></a>; Discussion
list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Saturday, 17 March 2012 6:06 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] Equilibriation nvt.mdp error<br>
</font> </div>
<br>
<meta content="off" http-equiv="x-dns-prefetch-control">
<div id="yiv1016666360">
<div>Hi Wholly,</div>
<div>It would be better to install a more recent version
of gromacs. The tutorial should state which version it
is written for.</div>
<div>Cheers,</div>
<div>Tsjerk</div>
<blockquote type="cite">On Mar 17, 2012 9:01 AM, "Wholly
Peach" <<a moz-do-not-send="true"
href="mailto:whollypeach@yahoo.com" rel="nofollow"
target="_blank" ymailto="mailto:whollypeach@yahoo.com">whollypeach@yahoo.com</a>>
wrote:<br>
<br>
<div>
<div style="font-family: Courier New, courier, monaco,
monospace, sans-serif; font-size: 12pt;">
<div><span>Dear All,</span></div>
<div><span></span> </div>
<div><span>I am running the on-line tutorial <a
moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html"
rel="nofollow" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html</a>.</span></div>
<div><span></span> </div>
<div>By "<font face="Arial">grompp -f nvt.mdp -c
em.gro -p topol.top -o nvt.tpr</font>", with the
nvt.mdp downloaded as attached following, I got
the following error message:</div>
<div> </div>
<div>"</div>
<div><font size="3">creating statusfile for 1
node...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">ERROR: invalid enum 'V-rescale'
for variable tcoupl, using 'No'</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Next time use one of: 'No'
'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Back Off! I just backed up
mdout.mdp to ./#mdout.mdp.14#</font></div>
<div><font size="3">
</font></div>
<div><font size="3">WARNING 1 [file nvt.mdp, line
unknown]:</font></div>
<div><font size="3">
</font></div>
<div><font size="3"> Unknown left-hand
'continuation' in parameter file</font></div>
<div><font size="3">
</font></div>
<div><font size="3">checking input for internal
consistency...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">calling cpp...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">processing topology...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Generated 165 of the 1596
non-bonded parameter combinations</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Excluding 3 bonded neighbours
for Protein_A 1</font></div>
<div><font size="3">
</font></div>
<div><font size="3">turning all bonds into
constraints...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Excluding 2 bonded neighbours
for SOL 10242</font></div>
<div><font size="3">
</font></div>
<div><font size="3">turning all bonds into
constraints...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Excluding 1 bonded neighbours
for NA+ 0</font></div>
<div><font size="3">
</font></div>
<div><font size="3">turning all bonds into
constraints...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Excluding 1 bonded neighbours
for CL- 8</font></div>
<div><font size="3">
</font></div>
<div><font size="3">turning all bonds into
constraints...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">processing coordinates...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">double-checking input for
internal consistency...</font></div>
<div><font size="3">
</font></div>
<div><font size="3">WARNING 2 [file "topol.top",
line 8274]:</font></div>
<div><font size="3">
</font></div>
<div><font size="3"> For energy conservation with
LINCS, lincs_iter should be 2 or larger.</font></div>
<div><font size="3">
</font></div>
<div><font size="3"> You can safely ignore this if
your system doesn't have any</font></div>
<div><font size="3">
</font></div>
<div><font size="3"> LINCS-constrained bonds;</font></div>
<div><font size="3">
</font></div>
<div><font size="3"> for water molecules we normally
use the analytical SETTLE algorithm</font></div>
<div><font size="3">
</font></div>
<div><font size="3"> instead.</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Setting gen_seed to 978754</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Velocities were taken from a
Maxwell distribution at 300 K</font></div>
<div><font size="3">
</font></div>
<div><font size="3">There were 2 warnings</font></div>
<div><font size="3">
</font></div>
<div><font size="3">-------------------------------------------------------</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Program grompp, VERSION 3.3.1</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Source code file: grompp.c,
line: 1109</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Fatal error:</font></div>
<div><font size="3">
</font></div>
<div><font size="3">There were 1 error(s) processing
your input</font></div>
<div><font size="3">
</font></div>
<div><font size="3">-------------------------------------------------------</font></div>
<div> </div>
<div>"</div>
<div> </div>
<div><span>I am looking forward to getting a message
on what is the problem.</span></div>
<div><span></span> </div>
<div><span>Cheers,</span></div>
<div><span>Wholly</span></div>
<div><span></span> </div>
<div><span><var></var></span> </div>
<div><span></span> </div>
<div><span>nvt.mdp:</span></div>
<div><span></span> </div>
<div><span>title = OPLS Lysozyme NVT equilibration
<br>
define = -DPOSRES ; position restrain the
protein<br>
; Run parameters<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>
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 <br>
constraints = all-bonds ; all bonds (even heavy
atom-H bonds) constrained<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>
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>
fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen
thermostat<br>
tc-grps = Protein Non-Protein ; two coupling
groups - more accurate<br>
tau_t = 0.1 0.1 ; time constant, in ps<br>
ref_t = 300 300 ; 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>
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</span></div>
<div><br>
</div>
</div>
</div>
<br>
--<br>
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