[gmx-users] newest version of gromacs under cygwin

[Mark Abraham]

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 <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 
>> <mailto: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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>
>
>
>

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