On 17/03/2012 7:29 PM, Wholly Peach wrote:
Dear All,
Will you please tell me the newest version of GROMACS that can be
installed under Cygwin?
4.5.5, per
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO
Your problems during make after correct configuration are probably
related to
http://x.cygwin.com/docs/faq/cygwin-x-faq.html#q-fork-failures, and will
be transient, as I have suggested to you before.
Mark
<http://x.cygwin.com/docs/faq/cygwin-x-faq.html#q-fork-failures>
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.
I am looking forward to getting a reply from you on it.
Cheers,
Wholly
*From:* Tsjerk Wassenaar <tsje...@gmail.com>
*To:* Wholly Peach <whollype...@yahoo.com>; Discussion list for
GROMACS users <gmx-users@gromacs.org>
*Sent:* Saturday, 17 March 2012 6:06 PM
*Subject:* Re: [gmx-users] Equilibriation nvt.mdp error
Hi Wholly,
It would be better to install a more recent version of gromacs. The
tutorial should state which version it is written for.
Cheers,
Tsjerk
On Mar 17, 2012 9:01 AM, "Wholly Peach" <whollype...@yahoo.com
<mailto:whollype...@yahoo.com>> wrote:
Dear All,
I am running the on-line tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html.
By "grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr", with the
nvt.mdp downloaded as attached following, I got the following error
message:
"
creating statusfile for 1 node...
ERROR: invalid enum 'V-rescale' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#
WARNING 1 [file nvt.mdp, line unknown]:
Unknown left-hand 'continuation' in parameter file
checking input for internal consistency...
calling cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 10242
turning all bonds into constraints...
Excluding 1 bonded neighbours for NA+ 0
turning all bonds into constraints...
Excluding 1 bonded neighbours for CL- 8
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
WARNING 2 [file "topol.top", line 8274]:
For energy conservation with LINCS, lincs_iter should be 2 or larger.
You can safely ignore this if your system doesn't have any
LINCS-constrained bonds;
for water molecules we normally use the analytical SETTLE algorithm
instead.
Setting gen_seed to 978754
Velocities were taken from a Maxwell distribution at 300 K
There were 2 warnings
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 1109
Fatal error:
There were 1 error(s) processing your input
-------------------------------------------------------
"
I am looking forward to getting a message on what is the problem.
Cheers,
Wholly
nvt.mdp:
title = OPLS Lysozyme NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
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