Could you unsubscribe me from this email chain? Thanks for all your help!
On Aug 11, 2010, at 1:31 AM, [email protected] wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: pulling simulation using implicit solvent in GROMACS > (Justin A. Lemkul) > 2. pulling simulation with implicit solvent (Samrat Pal) > 3. Error while trying free energy calculation (vivek sharma) > 4. Re: New beta release: 4.5-beta3 (Mark Abraham) > 5. dimer simulation ([email protected]) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Aug 2010 18:41:41 -0400 > From: "Justin A. Lemkul" <[email protected]> > Subject: [gmx-users] Re: pulling simulation using implicit solvent in > GROMACS > To: Samrat Pal <[email protected]>, "Gromacs Users' List" > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Please keep all Gromacs-related correspondence on the gmx-users list. > > Implicit solvent is available in the current 4.5 beta release. > > Another tip: the mailing list search would have turned this same answer up in > a > few seconds. This same question has been asked dozens of times. > > -Justin > > Samrat Pal wrote: >> Hi Justin, >> Is it possible to run pulling simulations using implicit >> solvent in GROAMCS? If yes, then can you please tell me what is the >> version? I am currently using GROMACS 4.0.7 and I found no option for >> implicit solvent in this version. >> Thanks >> Samrat >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 2 > Date: Tue, 10 Aug 2010 15:48:28 -0700 (PDT) > From: Samrat Pal <[email protected]> > Subject: [gmx-users] pulling simulation with implicit solvent > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > Can anyone please give me a mdp file for running pulling simulations > in implicit solvent using GROMACS? > Thanks in advance > Samrat > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100810/9d4f8b57/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 11 Aug 2010 10:13:48 +0530 > From: vivek sharma <[email protected]> > Subject: [gmx-users] Error while trying free energy calculation > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi There, > I was trying to run a free energy tutorial given at "* > http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial > *" > While trying the very first run i.e. mdrun using "*min_lbfgs0.mdp*" I ended > up with following error > ------------------------ > ERROR: With coulombtype = PME, rcoulomb must be equal to rlist > calling cpp... > ------------------------- > > which i know is valid while using PME for coulombic calculation, but when i > tried making rlist=rcoulomb, I got a warning as > -------------------------- > WARNING 1 [file min_lbfgs0.mdp, line unknown]: > For energy conservation with switch/shift potentials, rlist should be 0.1 > to 0.3 nm larger than rcoulomb/rvdw. > ----------------------------- > > following is the content of *min_lbfgs0.mdp > -------------------------**min_lbfgs0.mdp--------------------- > * > > ; RUN CONTROL PARAMETERS = > integrator = l-bfgs > nsteps = 5000 > ; Output frequency for energies to log file and energy file = > nstlog = 1 > nstenergy = 1 > ; ENERGY MINIMIZATION OPTIONS = > ; Force tolerance and initial step-size = > emtol = 100 > emstep = 0.01 > ; Max number of iterations in relax_shells = > niter = 20 > ; Number of correction steps to use for L-BFGS minimization > nbfgscorr = 10 > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 1 > ; ns algorithm (simple or grid) = > ns_type = grid > ; Periodic boundary conditions: xyz or none = > pbc = xyz > ; nblist cut-off = > rlist = 1.0 > domain-decomposition = no > ; OPTIONS FOR ELECTROSTATICS AND VDW = > ; Method for doing electrostatics = > coulombtype = pme > ;rcoulomb-switch = 0 > rcoulomb = 0.9 > ; Dielectric constant (DC) for cut-off or DC of reaction field = > epsilon-r = 1 > ; Method for doing Van der Waals = > vdw-type = switch > ; cut-off lengths = > rvdw-switch = 0.8 > rvdw = 0.9 > ; Apply long range dispersion corrections for Energy and Pressure = > DispCorr = EnerPres > ; Spacing for the PME/PPPM FFT grid = > fourierspacing = 0.1 > ; FFT grid size, when a value is 0 fourierspacing will be used = > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters = > pme_order = 6 > ewald_rtol = 1e-06 > epsilon_surface = 0 > optimize_fft = no > ; Free energy control stuff > free_energy = yes > init_lambda = 0.0 > delta_lambda = 0 > sc_alpha =0.5 > sc-power =1.0 > sc-sigma = 0.3 > -------------------------------------- > > Can anybody suggest whether the mdp file has some error or I can use > the one with the warning. > > > Thanks in advance, > Vivek > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100811/d1a2fc77/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Wed, 11 Aug 2010 14:59:13 +1000 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] New beta release: 4.5-beta3 > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > > > ----- Original Message ----- > From: Da-Wei Li <[email protected]> > Date: Wednesday, August 11, 2010 6:23 > Subject: Re: [gmx-users] New beta release: 4.5-beta3 > To: Discussion list for GROMACS users <[email protected]> > >> Hi,all >> >> Unfortunately, it still crash. Here it is the output of mdrun. Both >> Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use >> mvapich2 and intel compiler. > > MPICH variants are known to cause problems. Try OpenMPI. > > Mark > >> *************************** >> Getting Loaded... >> Reading file em.tpr, VERSION 4.5-beta3 (single precision) >> Loaded with Money >> >> >> Will use 9 particle-particle and 7 PME only nodes >> This is a guess, check the performance at the end of the log file >> Making 1D domain decomposition 9 x 1 x 1 >> >> Back Off! I just backed up em.trr to ./#em.trr.4# >> >> Back Off! I just backed up em.edr to ./#em.edr.4# >> >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+03 >> Number of steps >> = 50000 >> rank 9 in job 1 hpc-8-6.local_58777 caused >> collective abort of all ranks >> exit status of rank 9: killed by signal 9 >> >> ******************************* >> >> dawei >> >> On Tue, Aug 10, 2010 at 3:24 PM, Rossen Apostolov >> <[email protected]> wrote: >>> >>> New beta release of gromacs is available for testing: >>> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz. >>> >>> Many bugs have been fixed in this release, mainly double >> precision support >>> with icc compilers, SSE2. Have a look at the release note on >> the website for >>> more details. There are still some issues on Windows platofrms >> that will be >>> resolved before the final release. >>> >>> Please try it out and see if it works as expected! Hopefully >> there won't be >>> many more betas :)) >>> >>> Rossen >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search >> before posting! >>> Please don't post (un)subscribe requests to the list. Use the >> www interface >>> or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100811/8ba87152/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 11 Aug 2010 10:00:46 +0530 > From: [email protected] > Subject: [gmx-users] dimer simulation > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain;charset=utf-8 > > Dear gmx-users > I want to simulate a protein which biological function defined by dimer > formation. I need to simulate this protein in dimer as well as in > monomeric form to solve my objectives. I am using Gromacs-4.0.4 for > simulation. I have a doubt, is there any specific parameters for dimer > simulation or we have to use similar parameters like monomer protein > simulation. I read some literature's on dimer simulation but they are > using similar parameters like monomer. > -- > Regards > Sanjay Kumar Upadhyay > Research Scholor > Protein Dynamics lab > Dept of Chemistry > IIT Powai, Mumbai, 400076 > Ph no. 09920200345, 09699353562, > > > > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 76, Issue 51 > ***************************************** -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
