[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:
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> 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
>
>
>
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> ------------------------------
>
> 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
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> ------------------------------
>
> 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
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>> --
>> gmx-users mailing list gmx-users at gromacs.org
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> ------------------------------
>
> 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,
>
>
>
>
> ------------------------------
>
> --
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