[gmx-users] newest version of gromacs under cygwin

[Wholly Peach]

Dear All,
 
Will you please tell me the newest version of GROMACS that can be installed under Cygwin?
 
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 <tsjerkw at gmail.com>
To: Wholly Peach <whollypeach at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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" <whollypeach at 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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