[gmx-users] Unsubscribe

Peter Wilczynski pete.wilz at gmail.com
Wed Aug 11 17:51:54 CEST 2010


Could you unsubscribe me from this email chain?

Thanks for all your help!

On Aug 11, 2010, at 1:31 AM, gmx-users-request at gromacs.org wrote:

> Send gmx-users mailing list submissions to
> 	gmx-users at gromacs.org
> 
> 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
> 	gmx-users-request at gromacs.org
> 
> You can reach the person managing the list at
> 	gmx-users-owner at gromacs.org
> 
> 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 (sanjay23 at iitb.ac.in)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 10 Aug 2010 18:41:41 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: [gmx-users] Re: pulling simulation using implicit solvent in
> 	GROMACS
> To: Samrat Pal <psamrat10 at yahoo.com>,	"Gromacs Users' List"
> 	<gmx-users at gromacs.org>
> Message-ID: <4C61D5A5.7020308 at vt.edu>
> 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 <psamrat10 at yahoo.com>
> Subject: [gmx-users] pulling simulation with implicit solvent
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <850954.93026.qm at web120402.mail.ne1.yahoo.com>
> 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 <viveksharma.iitb at gmail.com>
> Subject: [gmx-users] Error while trying free energy calculation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<AANLkTikak1sbANGWS69qir2Qeu9p9RkSQv1ov3tTjzM9 at mail.gmail.com>
> 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 <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] New beta release: 4.5-beta3
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbb2a0566611e.4c62bac1 at anu.edu.au>
> Content-Type: text/plain; charset="us-ascii"
> 
> 
> 
> ----- Original Message -----
> From: Da-Wei Li <lidawei at gmail.com>
> Date: Wednesday, August 11, 2010 6:23
> Subject: Re: [gmx-users] New beta release: 4.5-beta3
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> 
>> 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
>> <rossen.apostolov at cbr.su.se> 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    gmx-users at gromacs.org
>>> 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 gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>> 
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> 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 gmx-users-request at gromacs.org.
>> 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: sanjay23 at iitb.ac.in
> Subject: [gmx-users] dimer simulation
> To: gmx-users at gromacs.org
> Message-ID: <7cf6b5fbb037efc7cbd770e479bfcec5.squirrel at gpo.iitb.ac.in>
> 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
> gmx-users at gromacs.org
> 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
> *****************************************




More information about the gromacs.org_gmx-users mailing list