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 <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> 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 > > >-- >gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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