<html><body><div style="color:#000; background-color:#fff; font-family:Courier New, courier, monaco, monospace, sans-serif;font-size:12pt"><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><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
size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <b><span style="font-weight: bold;">From:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> Wholly Peach <whollypeach@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <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 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 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>"<font size="1"></font></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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