[gmx-users] Re: Alternative TRP residue
Gerrit Groenhof
ggroenh at gwdg.de
Thu Jun 11 17:56:36 CEST 2009
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:
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> 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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>> *****************************************
>>
>>
>>
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>>
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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
>>
>>
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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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> *****************************************
--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/
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