[gmx-users] Re: Alternative TRP residue
abelius
abelius at gmail.com
Fri Jun 12 14:14:24 CEST 2009
Thank you for your reply,
I was just struggling to get the ffxxxbon.rtp syntax right since I only
have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines in
the ffxxxbon.rtp file?
#define <name> <distance in nm?> <?>
Furthermore where and how can I add the angle information?
Thanks,
Abel
Gerrit Groenhof wrote:
> You can use #define's
>
> Like
> [ bonds ]
> C1 C2 e_c1c2
>
> Then in the ffxxxbon.rtp
> you define these things explicitly
>
> #define e_c1c2 0.15 123445
>
> Gerrit
>
>
> On 11 Jun 2009, at 17:31, gmx-users-request at gromacs.org wrote:
>
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>> Today's Topics:
>>
>> 1. Re: Re: gmx-users Digest, Vol 62, Issue 57 (Justin A. Lemkul)
>> 2. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Thamu)
>> 3. Alternative TRP residue (abelius)
>> 4. Re: Issues regarding exclusions and Charge group distribution
>> (Manik Mayur)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 11 Jun 2009 10:50:29 -0400
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 62, Issue 57
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4A3119B5.30603 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>> Thamu wrote:
>>> Hi Mark,
>>>
>>> Yes I have compared the runtime for single as well as 8 processor .
>>> Could you please tell me the right steps to configure GROMACS-MPI
>>> version?.
>>>
>>
>> The full installation procedure is here:
>>
>> http://oldwww.gromacs.org/content/view/23/33/
>>
>> ...as well as Appendix A of the manual.
>>
>> -Justin
>>
>>> Thanks.
>>>
>>> thamu
>>>
>>> 2009/6/11 <gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>>
>>>
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>>> Today's Topics:
>>>
>>> 1. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Mark
>>> Abraham)
>>>
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Thu, 11 Jun 2009 13:56:15 +0000 (GMT)
>>> From: Mark Abraham <mark.abraham at anu.edu.au
>>> <mailto:mark.abraham at anu.edu.au>>
>>> Subject: Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow
>>> speed
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>>
>>> Message-ID: <fbe6b07c8ea.4a310cff at anu.edu.au
>>> <mailto:fbe6b07c8ea.4a310cff at anu.edu.au>>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> On 06/11/09, Thamu <asthamu at gmail.com <mailto:asthamu at gmail.com>>
>>> wrote:
>>>>
>>>> Hi Mark,
>>>>
>>>> The top md.log is below. The mdrun command was "mpirun -np 8
>>> ~/software/bin/mdrun_mpi -deffnm md"
>>> In my experience, correctly-configured MPI gromacs running in
>>> parallel reports information about the number of nodes and the
>>> identity of the node writing the .log file. This is missing, so
>>> something is wrong with your setup.
>>>
>>> I've assumed that you've compared this "8-processor" runtime with a
>>> single-processor runtime and found them comparable...
>>>
>>> Mark
>>>
>>>>
>>>>
>>>>
>>>> :-) G R O M A C S (-:
>>>>
>>>> GROup of MAchos and Cynical Suckers
>>>>
>>>> :-) VERSION 4.0.5 (-:
>>>>
>>>>
>>>> Written by David van der Spoel, Erik Lindahl, Berk Hess,
>>> and others.
>>>> Copyright (c) 1991-2000, University of Groningen, The
>>> Netherlands.
>>>> Copyright (c) 2001-2008, The GROMACS development team,
>>>> check out http://www.gromacs.org
>>> (http://www.gromacs.org) for more information.
>>>>
>>>> This program is free software; you can redistribute it
>>> and/or
>>>> modify it under the terms of the GNU General Public License
>>>> as published by the Free Software Foundation; either
>>> version 2
>>>> of the License, or (at your option) any later version.
>>>>
>>>> :-) /home/thamu/software/bin/mdrun_mpi (-:
>>>>
>>>>
>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
>>>> GROMACS 4: Algorithms for highly efficient, load-balanced, and
>>> scalable
>>>> molecular simulation
>>>> J. Chem. Theory Comput. 4 (2008) pp. 435-447
>>>> -------- -------- --- Thank You --- -------- --------
>>>>
>>>>
>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark
>>> and H. J. C.
>>>> Berendsen
>>>> GROMACS: Fast, Flexible and Free
>>>> J. Comp. Chem. 26 (2005) pp. 1701-1719
>>>> -------- -------- --- Thank You --- -------- --------
>>>>
>>>>
>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>> E. Lindahl and B. Hess and D. van der Spoel
>>>> GROMACS 3.0: A package for molecular simulation and trajectory
>>> analysis
>>>> J. Mol. Mod. 7 (2001) pp. 306-317
>>>> -------- -------- --- Thank You --- -------- --------
>>>>
>>>>
>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
>>>> GROMACS: A message-passing parallel molecular dynamics implementation
>>>> Comp. Phys. Comm. 91 (1995) pp. 43-56
>>>> -------- -------- --- Thank You --- -------- --------
>>>>
>>>> Input Parameters:
>>>> integrator = md
>>>> nsteps = 10000000
>>>> init_step = 0
>>>> ns_type = Grid
>>>> nstlist = 10
>>>> ndelta = 2
>>>> nstcomm = 1
>>>> comm_mode = Linear
>>>> nstlog = 100
>>>> nstxout = 1000
>>>> nstvout = 0
>>>> nstfout = 0
>>>> nstenergy = 100
>>>> nstxtcout = 0
>>>> init_t = 0
>>>> delta_t = 0.002
>>>> xtcprec = 1000
>>>> nkx = 70
>>>> nky = 70
>>>> nkz = 70
>>>> pme_order = 4
>>>> ewald_rtol = 1e-05
>>>> ewald_geometry = 0
>>>> epsilon_surface = 0
>>>> optimize_fft = TRUE
>>>> ePBC = xyz
>>>> bPeriodicMols = FALSE
>>>> bContinuation = FALSE
>>>> bShakeSOR = FALSE
>>>> etc = V-rescale
>>>> epc = Parrinello-Rahman
>>>> epctype = Isotropic
>>>> tau_p = 0.5
>>>> ref_p (3x3):
>>>> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
>>>> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
>>>> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
>>>> compress (3x3):
>>>> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
>>>> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
>>>> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
>>>> refcoord_scaling = No
>>>> posres_com (3):
>>>> posres_com[0]= 0.00000e+00
>>>> posres_com[1]= 0.00000e+00
>>>> posres_com[2]= 0.00000e+00
>>>> posres_comB (3):
>>>> posres_comB[0]= 0.00000e+00
>>>> posres_comB[1]= 0.00000e+00
>>>> posres_comB[2]= 0.00000e+00
>>>> andersen_seed = 815131
>>>> rlist = 1
>>>> rtpi = 0.05
>>>> coulombtype = PME
>>>> rcoulomb_switch = 0
>>>> rcoulomb = 1
>>>> vdwtype = Cut-off
>>>> rvdw_switch = 0
>>>> rvdw = 1.4
>>>> epsilon_r = 1
>>>> epsilon_rf = 1
>>>> tabext = 1
>>>> implicit_solvent = No
>>>> gb_algorithm = Still
>>>> gb_epsilon_solvent = 80
>>>> nstgbradii = 1
>>>> rgbradii = 2
>>>> gb_saltconc = 0
>>>> gb_obc_alpha = 1
>>>> gb_obc_beta = 0.8
>>>> gb_obc_gamma = 4.85
>>>> sa_surface_tension = 2.092
>>>> DispCorr = No
>>>> free_energy = no
>>>> init_lambda = 0
>>>> sc_alpha = 0
>>>> sc_power = 0
>>>> sc_sigma = 0.3
>>>> delta_lambda = 0
>>>> nwall = 0
>>>> wall_type = 9-3
>>>> wall_atomtype[0] = -1
>>>> wall_atomtype[1] = -1
>>>> wall_density[0] = 0
>>>> wall_density[1] = 0
>>>> wall_ewald_zfac = 3
>>>> pull = no
>>>> disre = No
>>>> disre_weighting = Conservative
>>>> disre_mixed = FALSE
>>>> dr_fc = 1000
>>>> dr_tau = 0
>>>> nstdisreout = 100
>>>> orires_fc = 0
>>>> orires_tau = 0
>>>> nstorireout = 100
>>>> dihre-fc = 1000
>>>> em_stepsize = 0.01
>>>> em_tol = 10
>>>> niter = 20
>>>> fc_stepsize = 0
>>>> nstcgsteep = 1000
>>>> nbfgscorr = 10
>>>> ConstAlg = Lincs
>>>> shake_tol = 0.0001
>>>> lincs_order = 4
>>>> lincs_warnangle = 30
>>>> lincs_iter = 1
>>>> bd_fric = 0
>>>> ld_seed = 1993
>>>> cos_accel = 0
>>>> deform (3x3):
>>>> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>> userint1 = 0
>>>> userint2 = 0
>>>> userint3 = 0
>>>> userint4 = 0
>>>> userreal1 = 0
>>>> userreal2 = 0
>>>> userreal3 = 0
>>>> userreal4 = 0
>>>> grpopts:
>>>> nrdf: 6706.82 106800
>>>> ref_t: 300 300
>>>> tau_t: 0.1 0.1
>>>> anneal: No No
>>>> ann_npoints: 0 0
>>>> acc: 0 0 0
>>>> nfreeze: N N N
>>>> energygrp_flags[ 0]: 0 0 0
>>>> energygrp_flags[ 1]: 0 0 0
>>>> energygrp_flags[ 2]: 0 0 0
>>>> efield-x:
>>>> n = 0
>>>> efield-xt:
>>>> n = 0
>>>> efield-y:
>>>> n = 0
>>>> efield-yt:
>>>> n = 0
>>>> efield-z:
>>>> n = 0
>>>> efield-zt:
>>>> n = 0
>>>> bQMMM = FALSE
>>>> QMconstraints = 0
>>>> QMMMscheme = 0
>>>> scalefactor = 1
>>>> qm_opts:
>>>> ngQM = 0
>>>> Table routines are used for coulomb: TRUE
>>>> Table routines are used for vdw: FALSE
>>>> Will do PME sum in reciprocal space.
>>>>
>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L.
>>> G. Pedersen
>>>> A smooth particle mesh Ewald method
>>>> J. Chem. Phys. 103 (1995) pp. 8577-8592
>>>> -------- -------- --- Thank You --- -------- --------
>>>>
>>>> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
>>>> Cut-off's: NS: 1 Coulomb: 1 LJ: 1.4
>>>> System total charge: -0.000
>>>> Generated table with 1200 data points for Ewald.
>>>> Tabscale = 500 points/nm
>>>> Generated table with 1200 data points for LJ6.
>>>> Tabscale = 500 points/nm
>>>> Generated table with 1200 data points for LJ12.
>>>> Tabscale = 500 points/nm
>>>> Generated table with 1200 data points for 1-4 COUL.
>>>> Tabscale = 500 points/nm
>>>> Generated table with 1200 data points for 1-4 LJ6.
>>>> Tabscale = 500 points/nm
>>>> Generated table with 1200 data points for 1-4 LJ12.
>>>> Tabscale = 500 points/nm
>>>>
>>>> Enabling TIP4p water optimization for 17798 molecules.
>>>>
>>>> Configuring nonbonded kernels...
>>>> Testing x86_64 SSE support... present.
>>>>
>>>>
>>>> Removing pbc first time
>>>>
>>>> Initializing LINear Constraint Solver
>>>>
>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
>>>> LINCS: A Linear Constraint Solver for molecular simulations
>>>> J. Comp. Chem. 18 (1997) pp. 1463-1472
>>>> -------- -------- --- Thank You --- -------- --------
>>>>
>>>> The number of constraints is 3439
>>>>
>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>> S. Miyamoto and P. A. Kollman
>>>> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms
>>> for Rigid
>>>> Water Models
>>>> J. Comp. Chem. 13 (1992) pp. 952-962
>>>> -------- -------- --- Thank You --- -------- --------
>>>>
>>>> Center of mass motion removal mode is Linear
>>>> We have the following groups for center of mass motion removal:
>>>> 0: rest
>>>>
>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>> G. Bussi, D. Donadio and M. Parrinello
>>>> Canonical sampling through velocity rescaling
>>>> J. Chem. Phys. 126 (2007) pp. 014101
>>>> -------- -------- --- Thank You --- -------- --------
>>>>
>>>> There are: 56781 Atoms
>>>> There are: 17798 VSites
>>>> Max number of connections per atom is 59
>>>> Total number of connections is 216528
>>>> Max number of graph edges per atom is 4
>>>> Total number of graph edges is 113666
>>>>
>>>> Constraining the starting coordinates (step 0)
>>>>
>>>> Constraining the coordinates at t0-dt (step 0)
>>>> RMS relative constraint deviation after constraining: 3.77e-05
>>>> Initial temperature: 299.838 K
>>>>
>>>>
>>>>>> Recently I successfully installed the gromacs-4.0.5 mpi version.
>>>>>> I could run in 8 cpu. but the speed is very slow.
>>>>>> Total number of atoms in the system is 78424.
>>>>>> while running all 8 cpu showing 95-100% CPU.
>>>>>>
>>>>>> How to speed up the calculation.
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>> That's normal for a system that atoms/cpu ratio.
>>>>> What's your system and what mdp file are you using?
>>>>> --
>>>>> ------------------------------------------------------
>>>>> You haven't given us any diagnostic information. The problem
>>> could be
>>>>> that you're not running an MPI GROMACS (show us your configure
>>> line,
>>>>> your mdrun command line and the top 50 lines of your .log file).
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
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>>> End of gmx-users Digest, Vol 62, Issue 57
>>> *****************************************
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> 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: Thu, 11 Jun 2009 22:53:54 +0800
>> From: Thamu <asthamu at gmail.com>
>> Subject: [gmx-users] Re: gromacs-4.0.5 parallel run in 8 cpu: slow
>> speed
>> To: gmx-users at gromacs.org
>> Message-ID:
>> <ca6f18140906110753r3acfd68wefc313a65f5ad9c at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi,
>>
>>
>>> i am using openmpi, how to build hostfile and where keep that file
>>>
>>> thamu
>>>
>>>
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 11 Jun 2009 17:09:41 +0200
>> From: abelius <abelius at gmail.com>
>> Subject: [gmx-users] Alternative TRP residue
>> To: gmx-users at gromacs.org
>> Message-ID: <4A311E35.7090709 at gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Dear All,
>>
>> I have AmberFF parameters for a TRP excited state and I was wondering if
>> it was possible to create an alternative TRP residue for gromacs?
>> Things I've done so far:
>> * Download and install amber99 for gromacs
>> * Add a new residue [ ETRP ] with adapted charges to the amber99.rtp
>> file
>> * Add ETRP to aminoacids.dat
>>
>> My question is where do I go from here, how can I add distances (bond
>> lengths) and angles?
>>
>> Thank you very much,
>> Abel
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 11 Jun 2009 21:00:02 +0530
>> From: Manik Mayur <manik.mayur at gmail.com>
>> Subject: [gmx-users] Re: Issues regarding exclusions and Charge group
>> distribution
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID:
>> <7e56bc410906110830g2208ebcak4a42fa9fb31777df at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi,
>>
>> The last mail supposedly bounced from the server due to attachments. So
>> please excuse in case you find this as a repetition.
>>
>> I am trying to simulate a system where I want to exclude all nb
>> interactions
>> between frozen groups. So I followed the manual and defined them in
>> energygrp_excl. But upon doing that it throws the following warning.
>>
>> WARNING 1 [file topol.top, line 1583]:
>> Can not exclude the lattice Coulomb energy between energy groups
>>
>> What is the reason of the warning and should I be worried about it or
>> safely
>> ignore it.
>>
>> Next, I am facing a strange problem with mdrun_mpi. If I run it on 4
>> nodes
>> then it throws up the following error. Which I traced to md.log where
>> I saw:
>>
>> There are: 15923 Atoms
>> Charge group distribution at step 0: 0 3264 3185 0 (why these zeroes?)
>> Grid: 3 x 4 x 5 cells
>>
>> However with 2 nodes it has and runs fine:
>>
>> There are: 15923 Atoms
>> Charge group distribution at step 0: 3226 3223
>> Grid: 4 x 5 x 25 cells
>>
>> The error-
>>
>> Making 1D domain decomposition 1 x 1 x 4
>> starting mdrun 'TransverseElectrode'
>> 100000 steps, 200.0 ps.
>> step 0
>>
>> NOTE: Turning on dynamic load balancing
>>
>> [md-comp1:32374] *** Process received signal ***
>> [md-comp1:32377] *** Process received signal ***
>> [md-comp1:32377] Signal: Segmentation fault (11)
>> [md-comp1:32377] Signal code: Address not mapped (1)
>> [md-comp1:32377] Failing at address: (nil)
>> [md-comp1:32374] Signal: Segmentation fault (11)
>> [md-comp1:32374] Signal code: Address not mapped (1)
>> [md-comp1:32374] Failing at address: (nil)
>> [md-comp1:32377] [ 0] [0xb7fd8440]
>> [md-comp1:32374] [ 0] [0xb7ef0440]
>> [md-comp1:32374] *** End of error message ***
>> [md-comp1:32377] *** End of error message ***
>>
>> I would be extremely thankful, if somebody points me to the source of
>> the
>> error and the workaround.
>>
>> Thanks,
>>
>> Manik Mayur
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>> INDIA
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>>
>> _______________________________________________
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>> 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 62, Issue 59
>> *****************************************
>
> --
> Gerrit Groenhof
> MPI biophysical chemistry
> Goettingen
> Germany
> http://wwwuser.gwdg.de/~ggroenh/
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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