[gmx-users] installation
hi,I i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've followed all the instructions given in the manual as well as in the website. ialso have installed fftw,its compiling with no problem. . but whenever i run pdb2gmx or command lke that its giving an error command not found. a little help regarding this matter will be very encouraging. thankx Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation
On Tue, Jun 2, 2009 at 12:21 PM, Samik Bhattacharya samikb...@yahoo.co.inwrote: hi,I i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've followed all the instructions given in the manual as well as in the website. ialso have installed fftw,its compiling with no problem. . but whenever i run pdb2gmx or command lke that its giving an error command not found. a little help regarding this matter will be very encouraging. Have you executed make links ? thankx Shamik -- Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here!http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation
Samik Bhattacharya wrote: hi,I i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've followed all the instructions given in the manual as well as in the website. ialso have installed fftw,its compiling with no problem. . but whenever i run pdb2gmx or command lke that its giving an error command not found. a little help regarding this matter will be very encouraging. The instructions here will probably help http://wiki.gromacs.org/index.php/Installation Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fwd: Segmentation fault while running gromacs 4.0.4
Dept. Biotechnology
Ext. 3108
- Forwarded Message -
From: Ms. Aswathy S aswat...@amritapuri.amrita.edu
To: gmx-users@gromacs.org
Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Segmentation fault while running gromacs 4.0.4
Hi,
I am working in GROMACS 4.0.4 and trying to do a receptor -ligand simulation.
But when I run the grommp for equilibration of about 30 ps, it shows
Segmentaion Fault. I din't get any idea that what type of error it causing from
the log file. When i run the free command it has a free space of 33 MB. Is that
could be the reason?. But I already read that gromacs doesnot consume that much
memory(10-20Mb). If so tell me what could be the possibilities. attaching the
mdp file and log file
I will explain all the steps i have did,
1. The protein and ligand i minimized in vaccum.
2. Then added water and again minimized the whole system (During both 1 2
minimization, Steepest Descents converged to machine precision in early steps
)
3. I used the otput file from the above result for equilibration steps(is that
the reason??!!!)
then i faced the segmentatuion fault. Please help me
thanks in advance
Dept. Biotechnology
Ext. 3108
Log file opened on Mon Jun 1 11:53:59 2009
Host: localhost.localdomain pid: 8316 nodeid: 0 nnodes: 1
The Gromacs distribution was built Wed May 13 12:15:31 IST 2009 by
r...@localhost.localdomain (Linux 2.6.18-92.el5xen i686)
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.4 (-:
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 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.
:-) mdrun (-:
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 = 5000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 100
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy= 10
nstxtcout= 100
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 60
nky = 60
nkz = 60
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p= 0.5
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
Re: [gmx-users] Fwd: Segmentation fault while running gromacs 4.0.4
Ms. Aswathy S wrote: Dept. Biotechnology Ext. 3108 - Forwarded Message - From: Ms. Aswathy S aswat...@amritapuri.amrita.edu To: gmx-users@gromacs.org Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Segmentation fault while running gromacs 4.0.4 Hi, I am working in GROMACS 4.0.4 and trying to do a receptor -ligand simulation. But when I run the grommp for equilibration of about 30 ps, it shows Segmentaion Fault. I din't get any idea that what type of error it causing from the log file. When i run the free command it has a free space of 33 MB. Is that could be the reason?. But I already read that gromacs doesnot consume that much memory(10-20Mb). If so tell me what could be the possibilities. attaching the mdp file and log file I will explain all the steps i have did, 1. The protein and ligand i minimized in vaccum. 2. Then added water and again minimized the whole system (During both 1 2 minimization, Steepest Descents converged to machine precision in early steps ) 3. I used the otput file from the above result for equilibration steps(is that the reason??!!!) then i faced the segmentatuion fault. Please help me Your simulation is blowing up http://wiki.gromacs.org/index.php/blowing_up, probably because your starting structure is badly broken (huge energy components, infinite temperature). Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] plain cutoff coulomb
Hi all, This seems like a really simple and silly question, but I have read through the manual and the archives and can't seem to find anything about it. If I were to set coulombtype = cutoff, g_energy will still calculate Coul-LR term which suggests that Gromacs calculates some long range correction term for the coulomb interactions beyond the cut-off rcoulomb. But I can't seem to find any explanation on how the interactions beyond rcoulomb is calculated when not using Ewald or PME. Can anyone enlighten me? Thank you! This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] plain cutoff coulomb
Cheong Wee Loong, Daniel wrote: Hi all, This seems like a really simple and silly question, but I have read through the manual and the archives and can’t seem to find anything about it. If I were to set coulombtype = cutoff, g_energy will still calculate Coul-LR term which suggests that Gromacs calculates some long range correction term for the coulomb interactions beyond the cut-off rcoulomb. But I can’t seem to find any explanation on how the interactions beyond rcoulomb is calculated when not using Ewald or PME. Can anyone enlighten me? GROMACS uses twin-range cutoffs, so the LR term exists when coulombtype = cutoff, rlist rcoulomb, and is updated on nstlist steps, or something similar. Search for twin-range in the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs 4.0.4 problem in extending MARTINI run by 600 ns, but no problem extending run by 60 ns using tpbconv
Dear All, I have run into this problem while using tpbconv. I typically write a new set of output files every ~ 600 ns. However, after about 108 repeats, tpbconv fails to write a new .tpr file: ### tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr ... ... Reading toplogy and shit from poptocg25-108.tpr Reading file poptocg25-108.tpr, VERSION 4.0.4 (single precision) Extending remaining runtime of by 60 ps (now -2134967296 steps) You've simulated long enough. Not writing tpr file ### However, there is no problem if I try to extend the run by only 60 ns? ### tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr ... ... Reading toplogy and shit from poptocg25-108.tpr Reading file poptocg25-108.tpr, VERSION 4.0.4 (single precision) Extending remaining runtime of by 6 ps (now 214200 steps) Writing statusfile with starting step 0 and length 214200 steps... time 0.000 and length 6426.000 ps ### Thank you for the help, -himanshu ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 4.0.4 problem in extending MARTINI run by 600 ns, but no problem extending run by 60 ns using tpbconv
himanshu khandelia wrote: Dear All, I have run into this problem while using tpbconv. I typically write a new set of output files every ~ 600 ns. However, after about 108 repeats, tpbconv fails to write a new .tpr file: ### tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr ... ... Reading toplogy and shit from poptocg25-108.tpr Reading file poptocg25-108.tpr, VERSION 4.0.4 (single precision) Extending remaining runtime of by 60 ps (now -2134967296 steps) There's the problem. The variable that counts the number of steps is signed, and has overflowed. It seems even a long variable is not enough for CG simulations :-) Please post a bugzilla and it will get fixed for the next version. Meantime, you can work around the situation by building a new .tpr that continues from your last endpoint. Mark You've simulated long enough. Not writing tpr file ### However, there is no problem if I try to extend the run by only 60 ns? ### tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr ... ... Reading toplogy and shit from poptocg25-108.tpr Reading file poptocg25-108.tpr, VERSION 4.0.4 (single precision) Extending remaining runtime of by 6 ps (now 214200 steps) Writing statusfile with starting step 0 and length 214200 steps... time 0.000 and length 6426.000 ps ### Thank you for the help, -himanshu ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation
Hello! Just like Manik Mayur suggested, the problem should be the links: Gromacs gives you the possibility to create links to /usr/bin directory (ot something similar). If you didn't do that, one of the option is trying to run the programs using the full path. Instead of using pdb2gmx, try to use /usr/local/gromacs/bin/pdb2gmx. Replace /usr/local/gromacs with the directory where you install gromacs. If you didn't choose anything it probably is /usr/local/gromacs. I hope this can help Nuno Azoia On Tue, 2009-06-02 at 12:21 +0530, Samik Bhattacharya wrote: hi,I i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've followed all the instructions given in the manual as well as in the website. ialso have installed fftw,its compiling with no problem. . but whenever i run pdb2gmx or command lke that its giving an error command not found. a little help regarding this matter will be very encouraging. thankx Shamik __ Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Nuno Gonçalo Azoia Lopes Finishing Research Laboratory Textile Engineering Department Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun seems stuck
Hello, I'd like to run a position restrained MD of a protein in water with 3000 (protein) + 4 (SOL) atoms. I preprocess the input with the command line: $grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro -p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr 4AKEprePRMD.mdp is: title = 4AKE_PRMD cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000 ; total 10.0 ps. nstcomm = 1; [steps] frequency for center of mass motion removal nstxout = 100 ; [steps] frequency to write coordinates to output trajectory file nstvout = 100 ; [steps] frequency to write velocities to output trajectory nstfout = 0; [steps] frequency to write forces to output trajectory nstlog = 10 ; [steps] frequency to write energies to log file nstenergy = 10 ; [steps] frequency to write energies to energy file nstlist = 5; neighbour searching ns_type = grid rlist = 1.0 coulombtype = EWALD rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = Protein Non-Protein ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL ; Pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ; [1/bar] compressibility of water ref_p = 1.0 ; [bar] reference pressure for coupling ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Then I run the PR MD: $grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e 4AKE_PRMD.edr -g 4AKE_PRMD.log -v These lines appear on the terminal: starting mdrun 'Protein in water' 5000 steps, 10.0 ps. ...but from this point on nothing more is displayed. I see neither steps nor time left. Are the parameter in the mdp file defining a too expensive simulation? I've tryied removing pressure and temperature coupling but the problem remains. How can I solve this issue? -DPOSRES refers to posre.itp, I guess. posre.itp was created from the original pdb before the energy minimization. Should I run pdb2gmx once again after the EM to create a new posre.itp? Thanks, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun seems stuck
Take a look to your .log file. Gromacs writes everything there. Nuno Azoia On Tue, 2009-06-02 at 10:45 +0100, Stefano Meliga wrote: Hello, I'd like to run a position restrained MD of a protein in water with 3000 (protein) + 4 (SOL) atoms. I preprocess the input with the command line: $grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro -p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr 4AKEprePRMD.mdp is: title = 4AKE_PRMD cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000 ; total 10.0 ps. nstcomm = 1; [steps] frequency for center of mass motion removal nstxout = 100 ; [steps] frequency to write coordinates to output trajectory file nstvout = 100 ; [steps] frequency to write velocities to output trajectory nstfout = 0; [steps] frequency to write forces to output trajectory nstlog = 10 ; [steps] frequency to write energies to log file nstenergy = 10 ; [steps] frequency to write energies to energy file nstlist = 5; neighbour searching ns_type = grid rlist = 1.0 coulombtype = EWALD rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = Protein Non-Protein ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL ; Pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ; [1/bar] compressibility of water ref_p = 1.0 ; [bar] reference pressure for coupling ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Then I run the PR MD: $grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e 4AKE_PRMD.edr -g 4AKE_PRMD.log -v These lines appear on the terminal: starting mdrun 'Protein in water' 5000 steps, 10.0 ps. ...but from this point on nothing more is displayed. I see neither steps nor time left. Are the parameter in the mdp file defining a too expensive simulation? I've tryied removing pressure and temperature coupling but the problem remains. How can I solve this issue? -DPOSRES refers to posre.itp, I guess. posre.itp was created from the original pdb before the energy minimization. Should I run pdb2gmx once again after the EM to create a new posre.itp? Thanks, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Nuno Gonçalo Azoia Lopes Finishing Research Laboratory Textile Engineering Department Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun seems stuck
The simulation seems just very slow. step 0 has appeared on the screen after several minutes and in the log file there's only step zero as well. Stefano Nuno Azoia ha scritto: Take a look to your .log file. Gromacs writes everything there. Nuno Azoia On Tue, 2009-06-02 at 10:45 +0100, Stefano Meliga wrote: Hello, I'd like to run a position restrained MD of a protein in water with 3000 (protein) + 4 (SOL) atoms. I preprocess the input with the command line: $grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro -p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr 4AKEprePRMD.mdp is: title = 4AKE_PRMD cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000 ; total 10.0 ps. nstcomm = 1; [steps] frequency for center of mass motion removal nstxout = 100 ; [steps] frequency to write coordinates to output trajectory file nstvout = 100 ; [steps] frequency to write velocities to output trajectory nstfout = 0; [steps] frequency to write forces to output trajectory nstlog = 10 ; [steps] frequency to write energies to log file nstenergy = 10 ; [steps] frequency to write energies to energy file nstlist = 5; neighbour searching ns_type = grid rlist = 1.0 coulombtype = EWALD rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = Protein Non-Protein ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL ; Pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ; [1/bar] compressibility of water ref_p = 1.0 ; [bar] reference pressure for coupling ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Then I run the PR MD: $grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e 4AKE_PRMD.edr -g 4AKE_PRMD.log -v These lines appear on the terminal: starting mdrun 'Protein in water' 5000 steps, 10.0 ps. ...but from this point on nothing more is displayed. I see neither steps nor time left. Are the parameter in the mdp file defining a too expensive simulation? I've tryied removing pressure and temperature coupling but the problem remains. How can I solve this issue? -DPOSRES refers to posre.itp, I guess. posre.itp was created from the original pdb before the energy minimization. Should I run pdb2gmx once again after the EM to create a new posre.itp? Thanks, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun seems stuck
On Tue, 2009-06-02 at 11:13 +0100, Stefano Meliga wrote: The simulation seems just very slow. step 0 has appeared on the screen after several minutes and in the log file there's only step zero as well. You have 43 000 atoms and are using Ewald summation which is O(N^2), so the simulation really is that slow. Switch to using coulombtype = PME, that should speed things up. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] segfault(11) -- simulation blows up on first step
Hi everyone!
I'm trying to run a simulation of a single diatomic Sulfur molecule. When I run
an equilibration scheme (generating velocities from a 300K Maxwell-Boltzmann
distribution) it runs fine, but when I take the equilibrated molecule and
couple one atom to a 0K heat bath (using Stochastic Dynamics) the simulation
segfaults at the first step.
I've enclosed as much information as I could. Notice (at the very bottom) that
the md.log file shows an initial temperature of 17884.7K, but already in the
report for step 0 the temperature, as well as many other thermodynamic
quantities, are NaN.
I've encountered one reference to the same error I'm getting, but itjust said
that there was some problem with the input files, but didn'tsay what was the
problem...
I hope you will find some stupid mistake in the *.mdp file, or something easily
remedied...
P.S.
I know GROMACS is not optimized for simulating tiny molecules, but I don't see
why it should be such a critical problem...
A wholotta supplemental data:
MDRUN_MPI STD-I/O:
==
step 0
[hydrogen:15285] *** Process received signal ***
[hydrogen:15285] Signal: Segmentation fault (11)
[hydrogen:15285] Signal code: Address not mapped (1)
[hydrogen:15285] Failing at address: 0xfffe16c50a90
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
[hydrogen:15285] *** End of error message ***
./test-2-6-09.sh: line 16: 15285 Segmentation fault mdrun_mpi -c md -v
MD.MDP
==
integrator=sd;stochastic dynamics (velocity Langevin) using a
leap-frog algorithm
dt=0.0001
nsteps=1; [steps] == total (nsteps*dt)
ps.
nstxout=1
nstvout=1
nstfout=1
; nstxtcout=1
nstenergy=1; write energies to energy file every 1000 steps
(default 100)
nstlog=1
energygrps=SLSR
ns_type=simple
periodic_molecules=no
coulombtype=PME
tc-grps=SLSR
tau_t=01; mass/gamma
ref_t=0 0; refference (bath) temperature
Pcoupl=no
gen_vel=no
gen_seed=-1; random seed based on computer clock
constraints=none
1S2.itp
===
[ atomtypes ]
;atomtype m (u) q (e)part.type V(cr)W(cr)
SX32.06000.000A1E-031E-05
[ moleculetype ]
; Name nrexcl
1S2 2
[ atoms ]
; nrtype resnr resid atom cgnr charge mass
1 SX 1 1S2 SL 10.000 32.0600
2 SX 1 1S2 SR 20.000 32.0600
[ bonds ]
; ai aj fuc0, c1, ...
1 2 20.2040 5.3E+60.2040 5.3E+6 ; SL SR
TRAJ.TRR
traj.trr frame 0:
natoms= 2 step= 0 time=0.000e+00 lambda= 0
box (3x3):
box[0]={ 6.37511e+00, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 6.37511e+00, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 6.37511e+00}
x (2x3):
x[0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00}
x[1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00}
v (2x3):
v[0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00}
v[1]={-2.22763e+00, 2.56083e-01, -1.38905e+00}
f (2x3):
f[0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03}
f[1]={-3.43615e+03, 2.13216e+02, -2.02509e+03}
MD.LOG
==
Input Parameters:
integrator = sd
nsteps = 1
init_step= 0
ns_type = Simple
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 1
nstxout = 1
nstvout = 1
nstfout = 1
nstenergy= 1
nstxtcout= 0
init_t = 0
delta_t = 0.0001
xtcprec = 1000
nkx = 54
nky = 54
nkz = 54
pme_order= 4
ewald_rtol = 1e-05
Re: [gmx-users] segfault(11) -- simulation blows up on first step
Hi,
I don't see any immediate problem in your file, except the fact that you
have to couple all molecule to a heat bath. Second, has much as I know, you
can't reach 0K, so what the meaning?
Best,
Itamar
On Tue, Jun 2, 2009 at 9:11 PM, Inon Sharony inons...@tau.ac.il wrote:
Hi everyone!
I'm trying to run a simulation of a single diatomic Sulfur molecule. When I
run an equilibration scheme (generating velocities from a 300K
Maxwell-Boltzmann distribution) it runs fine, but when I take the
equilibrated molecule and couple one atom to a 0K heat bath (using
Stochastic Dynamics) the simulation segfaults at the first step.
I've enclosed as much information as I could. Notice (at the very bottom)
that the md.log file shows an initial temperature of 17884.7K, but already
in the report for step 0 the temperature, as well as many other
thermodynamic quantities, are NaN.
I've encountered one reference to the same error I'm getting, but itjust
said that there was some problem with the input files, but didn'tsay what
was the problem...
I hope you will find some stupid mistake in the *.mdp file, or something
easily remedied...
P.S.
I know GROMACS is not optimized for simulating tiny molecules, but I don't
see why it should be such a critical problem...
A wholotta supplemental data:
MDRUN_MPI STD-I/O:
==
step 0
[hydrogen:15285] *** Process received signal ***
[hydrogen:15285] Signal: Segmentation fault (11)
[hydrogen:15285] Signal code: Address not mapped (1)
[hydrogen:15285] Failing at address: 0xfffe16c50a90
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x355b41d8b4]
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
[hydrogen:15285] *** End of error message ***
./test-2-6-09.sh: line 16: 15285 Segmentation fault mdrun_mpi -c md -v
MD.MDP
==
integrator=sd;stochastic dynamics (velocity Langevin) using a
leap-frog algorithm
dt=0.0001
nsteps=1; [steps] == total
(nsteps*dt) ps.
nstxout=1
nstvout=1
nstfout=1
; nstxtcout=1
nstenergy=1; write energies to energy file every 1000 steps
(default 100)
nstlog=1
energygrps=SLSR
ns_type=simple
periodic_molecules=no
coulombtype=PME
tc-grps=SLSR
tau_t=01; mass/gamma
ref_t=0 0; refference (bath) temperature
Pcoupl=no
gen_vel=no
gen_seed=-1; random seed based on computer clock
constraints=none
1S2.itp
===
[ atomtypes ]
;atomtype m (u) q (e)part.type V(cr)W(cr)
SX32.06000.000A1E-031E-05
[ moleculetype ]
; Name nrexcl
1S2 2
[ atoms ]
; nrtype resnr resid atom cgnr charge mass
1 SX 1 1S2 SL 10.000 32.0600
2 SX 1 1S2 SR 20.000 32.0600
[ bonds ]
; ai aj fuc0, c1, ...
1 2 20.2040 5.3E+60.2040 5.3E+6 ; SL SR
TRAJ.TRR
traj.trr frame 0:
natoms= 2 step= 0 time=0.000e+00 lambda=
0
box (3x3):
box[0]={ 6.37511e+00, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 6.37511e+00, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 6.37511e+00}
x (2x3):
x[0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00}
x[1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00}
v (2x3):
v[0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00}
v[1]={-2.22763e+00, 2.56083e-01, -1.38905e+00}
f (2x3):
f[0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03}
f[1]={-3.43615e+03, 2.13216e+02, -2.02509e+03}
MD.LOG
==
Input Parameters:
integrator = sd
nsteps = 1
init_step= 0
ns_type = Simple
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 1
nstxout
[gmx-users] segfault(11) -- simulation blows up on first step
Sorry for the previous mail, I guess the appended content was too long.
Anyway, here it is as an attached file
Sorry, and thanks again
--
Inon Sharony
ינון שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing this e-mail.
MDRUN_MPI STD-I/O:
==
step 0
[hydrogen:15285] *** Process received signal ***
[hydrogen:15285] Signal: Segmentation fault (11)
[hydrogen:15285] Signal code: Address not mapped (1)
[hydrogen:15285] Failing at address: 0xfffe16c50a90
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
[hydrogen:15285] *** End of error message ***
./test-2-6-09.sh: line 16: 15285 Segmentation fault mdrun_mpi -c md -v
MD.MDP
==
integrator = sd ;stochastic dynamics (velocity Langevin) using
a leap-frog algorithm
dt = 0.0001
nsteps = 1 ;
[steps] == total (nsteps*dt) ps.
nstxout = 1
nstvout = 1
nstfout = 1
; nstxtcout = 1
nstenergy = 1 ; write energies to energy file every 1000
steps (default 100)
nstlog = 1
energygrps = SL SR
ns_type = simple
periodic_molecules = no
coulombtype = PME
tc-grps = SL SR
tau_t = 0 1 ; mass/gamma
ref_t = 0 0 ; refference (bath) temperature
Pcoupl = no
gen_vel = no
gen_seed= -1 ; random seed based on computer clock
constraints = none
1S2.itp
===
[ atomtypes ]
;atomtype m (u) q (e) part.type V(cr) W(cr)
SX 32.0600 0.000 A 1E-03 1E-05
[ moleculetype ]
; Name nrexcl
1S2 2
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 SX 1 1S2 SL 10.000 32.0600
2 SX 1 1S2 SR 20.000 32.0600
[ bonds ]
; ai aj fuc0, c1, ...
1 2 20.2040 5.3E+60.2040 5.3E+6 ; SL SR
TRAJ.TRR
traj.trr frame 0:
natoms= 2 step= 0 time=0.000e+00 lambda= 0
box (3x3):
box[0]={ 6.37511e+00, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 6.37511e+00, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 6.37511e+00}
x (2x3):
x[0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00}
x[1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00}
v (2x3):
v[0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00}
v[1]={-2.22763e+00, 2.56083e-01, -1.38905e+00}
f (2x3):
f[0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03}
f[1]={-3.43615e+03, 2.13216e+02, -2.02509e+03}
MD.LOG
==
Input Parameters:
integrator = sd
nsteps = 1
init_step= 0
ns_type = Simple
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 1
nstxout = 1
nstvout = 1
nstfout = 1
nstenergy= 1
nstxtcout= 0
init_t = 0
delta_t = 0.0001
xtcprec = 1000
nkx = 54
nky = 54
nkz = 54
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = No
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00,
Re: [gmx-users] segfault(11) -- simulation blows up on first step
Inon Sharony wrote:
Hi everyone!
I'm trying to run a simulation of a single diatomic Sulfur molecule.
When I run an equilibration scheme (generating velocities from a 300K
Maxwell-Boltzmann distribution) it runs fine, but when I take the
equilibrated molecule and couple one atom to a 0K heat bath (using
Stochastic Dynamics) the simulation segfaults at the first step.
I've enclosed as much information as I could. Notice (at the very
bottom) that the md.log file shows an initial temperature of 17884.7K,
but already in the report for step 0 the temperature, as well as many
other thermodynamic quantities, are NaN.
I've encountered one reference to the same error I'm getting, but itjust
said that there was some problem with the input files, but didn'tsay
what was the problem...
I hope you will find some stupid mistake in the *.mdp file, or something
easily remedied...
P.S.
I know GROMACS is not optimized for simulating tiny molecules, but I
don't see why it should be such a critical problem...
A wholotta supplemental data:
snip
tau_t=01; mass/gamma
tau_t for the sd integrator is given in ps^-1; therefore a value of zero could
be causing the sd integrator to use some sort of infinite friction coefficient.
If you are trying to use tau_t = 0 to turn off temperature coupling, it may not
work with sd (not sure), or it could be causing some physically unrealistic
condition. Why would two bonded atoms experience different temperatures or
coupling/lack thereof?
-Justin
ref_t=0 0; refference (bath) temperature
Pcoupl=no
gen_vel=no
gen_seed=-1; random seed based on computer clock
constraints=none
1S2.itp
===
[ atomtypes ]
;atomtype m (u) q (e)part.type V(cr)W(cr)
SX32.06000.000A1E-031E-05
[ moleculetype ]
; Name nrexcl
1S2 2
[ atoms ]
; nrtype resnr resid atom cgnr charge mass
1 SX 1 1S2 SL 10.000 32.0600
2 SX 1 1S2 SR 20.000 32.0600
[ bonds ]
; ai aj fuc0, c1, ...
1 2 20.2040 5.3E+60.2040 5.3E+6 ; SL SR
TRAJ.TRR
traj.trr frame 0:
natoms= 2 step= 0 time=0.000e+00 lambda= 0
box (3x3):
box[0]={ 6.37511e+00, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 6.37511e+00, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 6.37511e+00}
x (2x3):
x[0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00}
x[1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00}
v (2x3):
v[0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00}
v[1]={-2.22763e+00, 2.56083e-01, -1.38905e+00}
f (2x3):
f[0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03}
f[1]={-3.43615e+03, 2.13216e+02, -2.02509e+03}
MD.LOG
==
Input Parameters:
integrator = sd
nsteps = 1
init_step= 0
ns_type = Simple
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 1
nstxout = 1
nstvout = 1
nstfout = 1
nstenergy= 1
nstxtcout= 0
init_t = 0
delta_t = 0.0001
xtcprec = 1000
nkx = 54
nky = 54
nkz = 54
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = No
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi = 0.05
coulombtype
[gmx-users] problem with generation of .gro file
Hello, I am running the pdb2gmx command for a homodimer protein with SF4 (a ferro-sulphur cluster) ligand but it fails to generate the .gro file. A error is coming SF4 not found in residue topology database. I have trired all the different force fields. Can anybody please tell me how to correct the error? How to modify the rtp file to consider the ligand? Subarna thakur University of north bengal Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo..com___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with generation of .gro file
subarna thakur wrote: Hello, I am running the pdb2gmx command for a homodimer protein with SF4 (a ferro-sulphur cluster) ligand but it fails to generate the .gro file. A error is coming SF4 not found in residue topology database. I have trired all the different force fields. Can anybody please tell me how to correct the error? How to modify the rtp file to consider the ligand? Dealing with the error: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database The unfortunate news that you have your work cut out for you: http://wiki.gromacs.org/index.php/Parameterization http://wiki.gromacs.org/index.php/Exotic_Species Parameterization is an advanced topic, especially when dealing with strange species like an iron-sulfur cluster. Read the exotic species article closely. -Justin Subarna thakur University of north bengal Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Normal of the benzene and z axis.
Dear gmx users;How can I calculate the angle distribution forthe angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] crystals of KCl during simulation
Hi Rebeca,
the paper David suggests is certainly more complete, I just compared OPLS
and Aqvist's parameters for sodium for the specific case of anionic
micelles. anyway, if want to try the Aqvist's parameters take a look
inside ffoplsaa.atp file (opls_408 for K+).
best regards,
André
Rebeca García Fandiño wrote:
Thank you very much, André. Could you please indicate me how could
I use these parameters in Gromacs? I have not seen them included in
ions.itp and I could not find anything in the manual.
Best wishes,
Rebeca.
I would recommend reading the following paper, even though it only is
about NaCl it compares the properties of four different parameter sets,
and IIRC Åqvist's parameters were not so great.
@Article{ Hess2006c,
author = B. Hess and C. Holm and N. {van der Vegt},
title =Osmotic coefficients of atomistic NaCl (aq) force
fields,
journal = J. Chem. Phys.,
year = 2006,
volume = 124,
pages =164509,
abstract = Solvated ions are becoming increasingly important
for (bio)molecular simulations. But there are not
much suitable data to validate the
intermediate-range solution structure that ion-water
force fields produce. We compare six selected
combinations of four biomolecular Na-Cl force fields
and four popular water models by means of effective
ion-ion potentials. First we derive an effective
potential at high dilution from simulations of two
ions in explicit water. At higher ionic
concentration multibody effects will become
important. We propose to capture those by employing
a concentration dependent dielectric
permittivity. With the so obtained effective
potentials we then perform implicit solvent
simulations. We demonstrate that our effective
potentials accurately reproduce ion-ion coordination
numbers and the local structure. They allow us
furthermore to calculate osmotic coefficients that
can be directly compared with experimental data. We
show that the osmotic coefficient is a sensitive and
accurate measure for the effective ion-ion
interactions and the intermediate-range structure of
the solution. It is therefore a suitable and useful
quantity for validating and parametrizing atomistic
ion-water force fields. (c) 2006 American Institute
of Physics. 0021-9606
}
Date: Mon, 1 Jun 2009 14:52:35 -0300
Subject: RE: [gmx-users] crystals of KCl during simulation
From: mo...@ufscar.br
To: gmx-users@gromacs.org
Hi Rebeca,
I found out a few years ago that OPLS parameters for Na+ were
inadequate
for my simulations on surfactants aggregation due to the formation of
stable (and unrealistic) ionic bridges. I got better structures using
Aqvist's parameters (available in GROMACS), maybe you could try these
parameters for K+ as well.
please let me know if that works.
best regards,
André
Yes, I use PME.
Date: Mon, 1 Jun 2009 19:34:27 +0200
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] crystals of KCl during simulation
Rebeca García Fandiño wrote:
Thank you very much for your answer. I have read some recent
literature,
and you are right, it is a problem about the parameters for ions
in
Amber.
I have found this paper:
Parameters of Monovalent Ions in the Amber-99 Forcefield:
Assesment of
Inaccuracies and Proposed Improvements
http://pubs.acs.org/doi/abs/10.1021/jp0765392
There, they simulate nucleic acids using a combination of Amber
and
OPLS sigma and epsilon for the ions. I have tried that in the
case of
my
protein, just changing the ion sigma and epsilon in the topology
by
those corresponding to OPLS, but I still observe aggregation for
the
ions.
Would this combination of Amber and OPLS have any kind of
potential
problem during the simulation? Has anybody any idea to avoid
this type
of artefact?
Just checking, do you use PME? (You should...)
Thank you very much in advance,
Rebeca.
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] crystals of KCl during simulation
Date: Mon, 1 Jun 2009 14:34:55 +0200
From: baa...@smplinux.de
Hi,
rega...@hotmail.com said:
[..] but after equilibration I have observed that KCl is
aggregating, like
if it was making
Re: [gmx-users] installation
Nuno Azoia wrote: Hello! Just like Manik Mayur suggested, the problem should be the links: Making links may fix the problem of finding executables if that link location is already in your path, but it won't fix your other environment variables, or perhaps if you used configure --prefix. Gromacs gives you the possibility to create links to /usr/bin directory (ot something similar). If you didn't do that, one of the option is trying to run the programs using the full path. Instead of using pdb2gmx, try to use /usr/local/gromacs/bin/pdb2gmx. Replace /usr/local/gromacs with the directory where you install gromacs. If you didn't choose anything it probably is /usr/local/gromacs. Call source /path/to/GMXRC, then go do science. Mark I hope this can help Nuno Azoia On Tue, 2009-06-02 at 12:21 +0530, Samik Bhattacharya wrote: hi,I i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've followed all the instructions given in the manual as well as in the website. ialso have installed fftw,its compiling with no problem. . but whenever i run pdb2gmx or command lke that its giving an error command not found. a little help regarding this matter will be very encouraging. thankx Shamik __ Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Normal of the benzene and z axis.
Eudes Fileti wrote: Dear gmx users; How can I calculate the angle distribution for the angle between the normal of the benzene and z axis? The function of various tools are discussed in section 8 of the manual. The clue you seek is there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs invsqrt() overlaps with icc invsqrt()
Hello, I have just compiled gromacs 4.0.4 using the intel compiler. While I believe that gromacs itself doesn't get a huge benefit from icc, fftw certainly does and it's on the order of a 10% speedup, which is significant enough for me to dedicate some time to getting this working. Problem is, invsqrt is defined both in gromacs and in the icc libraries, as is already known: http://www.gromacs.org/pipermail/gmx-users/2006-June/022009.html ../../../include/vec.h(152): warning #147: declaration is incompatible with double invsqrt(double) (declared at line 635 of /opt/sharcnet/intel/11.0.083/icc/include/math.h) static inline real invsqrt(real x) I have solved this problem by the following procedure: # #!/bin/bash for i in `find ./gromacs-4.0.4`; do sed 's/invsqrt/invSAFEsqrt/g' $i tmp; mv tmp $i; done chmod +x ./gromacs-4.0.4/configure mv ./gromacs-4.0.4/src/gmxlib/cinvsqrtdata.c ./gromacs-4.0.4/src/gmxlib/cinvSAFEsqrtdata.c # And it now compiles without warning. I was unable to link an icc-compiled fftw to a PGI or gcc compilation of gromacs, due to linking problems, although I imagine that that is possible. First, does anybody see any immediate problems with this? Second, is there still a motivation to get rid of this problem? Third, does anybody know how I can link an icc-compiled fftw to a PGI or gcc compilation of gromacs, and if there is any reason that this is a bad idea? Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dist
Dear Gromacs Users, I need to extract all possible distances between any two atom pairs of a small hexa- to dodecamer from a trajectory. The same is necessary for all dihedral angles of this protein. Now I wonder if this is possible without defining all of them manually in the ndx file and call g_dist for each of them ? Is there a short answer on that ? Maybe I missed the answer to that question in the forum ?! greetings, joern ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs invsqrt() overlaps with icc invsqrt()
chris.ne...@utoronto.ca wrote: Hello, I have just compiled gromacs 4.0.4 using the intel compiler. While I believe that gromacs itself doesn't get a huge benefit from icc, fftw certainly does and it's on the order of a 10% speedup, which is significant enough for me to dedicate some time to getting this working. Problem is, invsqrt is defined both in gromacs and in the icc libraries, as is already known: http://www.gromacs.org/pipermail/gmx-users/2006-June/022009.html ../../../include/vec.h(152): warning #147: declaration is incompatible with double invsqrt(double) (declared at line 635 of /opt/sharcnet/intel/11.0.083/icc/include/math.h) static inline real invsqrt(real x) I have solved this problem by the following procedure: # #!/bin/bash for i in `find ./gromacs-4.0.4`; do sed 's/invsqrt/invSAFEsqrt/g' $i tmp; mv tmp $i; done chmod +x ./gromacs-4.0.4/configure Using sed -i is a bit more elegant and keeps the permissions, IIRC. mv ./gromacs-4.0.4/src/gmxlib/cinvsqrtdata.c ./gromacs-4.0.4/src/gmxlib/cinvSAFEsqrtdata.c # And it now compiles without warning. I was unable to link an icc-compiled fftw to a PGI or gcc compilation of gromacs, due to linking problems, although I imagine that that is possible. First, does anybody see any immediate problems with this? Looks OK. Second, is there still a motivation to get rid of this problem? It seems reasonable to get the GROMACS function out of the standard namespace, or to test for and use a library function with configure. Third, does anybody know how I can link an icc-compiled fftw to a PGI or gcc compilation of gromacs, and if there is any reason that this is a bad idea? I would have expected it to just work, however I have had multiple inexplicable problems with various icc versions on IA64 hardware. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories
On 6/1/09 11:48 PM, Mark Abraham wrote:
Jinyao Wang wrote:
Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
but I am getting the following the fatal error:
Fatal error:
Library file aminoacids.dat not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
How can I solve it?
See
http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation
Mark
The procedure on that Wiki-Page actually works in (from my personal experience)
only ~90% of the cases:
After I installed Gromacs 4.0.5 on a Cluster in my home-directory, tools like
pdb2gmx kept complaining they couldn't find the topology files, as GMXLIB was
actually not set by GMXRC.
Fortunately adding the line:
export GMXLIB=${GMXDATA}/gromacs/top
just after sourcing GMXRC in my .bashrc, worked for me.
Oliver
___
gmx-users mailing listgmx-users@gromacs.org
http://www.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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation
On Wed, 2009-06-03 at 00:42 +1000, Mark Abraham wrote: Nuno Azoia wrote: Hello! Just like Manik Mayur suggested, the problem should be the links: Making links may fix the problem of finding executables if that link location is already in your path, but it won't fix your other environment variables, or perhaps if you used configure --prefix. Gromacs gives you the possibility to create links to /usr/bin directory (ot something similar). If you didn't do that, one of the option is trying to run the programs using the full path. Instead of using pdb2gmx, try to use /usr/local/gromacs/bin/pdb2gmx. Replace /usr/local/gromacs with the directory where you install gromacs. If you didn't choose anything it probably is /usr/local/gromacs. Call source /path/to/GMXRC, then go do science. That's what I love the most in this list, always learning something interesting. Thanks. Nuno Azoia Mark I hope this can help Nuno Azoia On Tue, 2009-06-02 at 12:21 +0530, Samik Bhattacharya wrote: hi,I i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've followed all the instructions given in the manual as well as in the website. ialso have installed fftw,its compiling with no problem. . but whenever i run pdb2gmx or command lke that its giving an error command not found. a little help regarding this matter will be very encouraging. thankx Shamik __ Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Computer simulation details
Hi everyone, I would like to run GPCR protein dynamics in lipid bilayer along with water molecules and ions. As you all know it becomes huge system and may take very long time to obtain results on ordinary PCs.I would like to run the above mentioned simulation on my personnel laptop. Please let me know your best suggestions from experience ,which one would be the most efficient to do the same, I mean the constitution of the laptop like GB in RAM, number of cores required, processor clock, 3D graphics compatability, hard disc size and finally the brand. Your suggestions would be of great help to many. Regards, Akula ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Computer simulation details
As you already pointed out, it may take a very long time on ordinary PCs. On a laptop it would take even longer ... Use a Linux workstation with 4 processor cores minimum. Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Pramod Akula Sent: 02 June 2009 17:07 To: gmx-users@gromacs.org Subject: [gmx-users] Computer simulation details Hi everyone, I would like to run GPCR protein dynamics in lipid bilayer along with water molecules and ions. As you all know it becomes huge system and may take very long time to obtain results on ordinary PCs.I would like to run the above mentioned simulation on my personnel laptop. Please let me know your best suggestions from experience ,which one would be the most efficient to do the same, I mean the constitution of the laptop like GB in RAM, number of cores required, processor clock, 3D graphics compatability, hard disc size and finally the brand. Your suggestions would be of great help to many. Regards, Akula ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] crystals of KCl during simulation
Thank you very much for your answers. Anyway, if I want to simulate my protein
with Amber, would it be a big problem to combine parameter from Amber with
parameters from OPLS for water and/or ions?
Best wishes,
Rebeca.
Date: Tue, 2 Jun 2009 09:51:12 -0300
Subject: Re: [gmx-users] crystals of KCl during simulation
From: mo...@ufscar.br
To: gmx-users@gromacs.org
Hi Rebeca,
the paper David suggests is certainly more complete, I just compared OPLS
and Aqvist's parameters for sodium for the specific case of anionic
micelles. anyway, if want to try the Aqvist's parameters take a look
inside ffoplsaa.atp file (opls_408 for K+).
best regards,
André
Rebeca García Fandiño wrote:
Thank you very much, André. Could you please indicate me how could
I use these parameters in Gromacs? I have not seen them included in
ions.itp and I could not find anything in the manual.
Best wishes,
Rebeca.
I would recommend reading the following paper, even though it only is
about NaCl it compares the properties of four different parameter sets,
and IIRC Åqvist's parameters were not so great.
@Article{ Hess2006c,
author = B. Hess and C. Holm and N. {van der Vegt},
title = Osmotic coefficients of atomistic NaCl (aq) force
fields,
journal = J. Chem. Phys.,
year = 2006,
volume = 124,
pages = 164509,
abstract = Solvated ions are becoming increasingly important
for (bio)molecular simulations. But there are not
much suitable data to validate the
intermediate-range solution structure that ion-water
force fields produce. We compare six selected
combinations of four biomolecular Na-Cl force fields
and four popular water models by means of effective
ion-ion potentials. First we derive an effective
potential at high dilution from simulations of two
ions in explicit water. At higher ionic
concentration multibody effects will become
important. We propose to capture those by employing
a concentration dependent dielectric
permittivity. With the so obtained effective
potentials we then perform implicit solvent
simulations. We demonstrate that our effective
potentials accurately reproduce ion-ion coordination
numbers and the local structure. They allow us
furthermore to calculate osmotic coefficients that
can be directly compared with experimental data. We
show that the osmotic coefficient is a sensitive and
accurate measure for the effective ion-ion
interactions and the intermediate-range structure of
the solution. It is therefore a suitable and useful
quantity for validating and parametrizing atomistic
ion-water force fields. (c) 2006 American Institute
of Physics. 0021-9606
}
Date: Mon, 1 Jun 2009 14:52:35 -0300
Subject: RE: [gmx-users] crystals of KCl during simulation
From: mo...@ufscar.br
To: gmx-users@gromacs.org
Hi Rebeca,
I found out a few years ago that OPLS parameters for Na+ were
inadequate
for my simulations on surfactants aggregation due to the formation of
stable (and unrealistic) ionic bridges. I got better structures using
Aqvist's parameters (available in GROMACS), maybe you could try these
parameters for K+ as well.
please let me know if that works.
best regards,
André
Yes, I use PME.
Date: Mon, 1 Jun 2009 19:34:27 +0200
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] crystals of KCl during simulation
Rebeca García Fandiño wrote:
Thank you very much for your answer. I have read some recent
literature,
and you are right, it is a problem about the parameters for ions
in
Amber.
I have found this paper:
Parameters of Monovalent Ions in the Amber-99 Forcefield:
Assesment of
Inaccuracies and Proposed Improvements
http://pubs.acs.org/doi/abs/10.1021/jp0765392
There, they simulate nucleic acids using a combination of Amber
and
OPLS sigma and epsilon for the ions. I have tried that in the
case of
my
protein, just changing the ion sigma and epsilon in the topology
by
those corresponding to OPLS, but I still observe aggregation for
the
ions.
Would this combination of Amber and OPLS have any kind of
potential
problem during the simulation? Has anybody any idea to avoid
this type
of artefact?
Just checking, do you use PME? (You should...)
Thank you very much in advance,
Rebeca.
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] crystals of KCl during simulation
Date: Mon, 1 Jun 2009 14:34:55 +0200
From: baa...@smplinux.de
Hi,
rega...@hotmail.com said:
[..] but after equilibration I have observed that KCl is
aggregating, like
if it was making crystals. When I used NaCl instead KCl,
this not
happened.
Does anybody has any idea about the reason of
[gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)
Dear GROMACS users, I have been trying to expand a membrane by a non-integer multiplier (for example X1.5). This can be done using genbox -cs Membrane.gro -o Expanded_membrane.gro -box 1.5X 1.5Y Z This has worked very good with homogenous membranes, and only very short equilibrium times were required to re-equilibrate the membrane (~10-20ns). Now I am trying to deal the same way with heterogeneous membrane (POPG/POPE mixture, Mikko Karttunen et. al). When trying to invoke the above command to the POPG/POPE membrane I get a membrane with different compositions of lipids in the upper and lower leaflets. This happens (so I suspect) because the arrangement of lipids in each leaflet is somewhat different so that the molecules that get' to be multiplied do not conserve the same ratio of different lipids as in the original structure (which has ratio of 1:3 POPG/POPE). Is there a way to multiply the membrane by a non-integer number AND somehow conserve the ratio of different lipid species too? Or at the very least, to have both upper and lower leaflets identical after multiplication? (This, too, would help immensely). Thanks, -Shay ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)
Shay Amram wrote: Dear GROMACS users, I have been trying to expand a membrane by a non-integer multiplier (for example X1.5). This can be done using *genbox -cs Membrane.gro -o Expanded_membrane.gro –box 1.5X 1.5Y Z*** This has worked very good with _homogenous_ membranes, and only very short equilibrium times were required to re-equilibrate the membrane (~10-20ns). Now I am trying to deal the same way with _heterogeneous_ membrane (POPG/POPE mixture, Mikko Karttunen et. al). When trying to invoke the above command to the POPG/POPE membrane I get a membrane with different compositions of lipids in the upper and lower leaflets. This happens (so I suspect) because the arrangement of lipids in each leaflet is somewhat different so that the molecules that get' to be multiplied do not conserve the same ratio of different lipids as in the original structure (which has ratio of 1:3 POPG/POPE). If you have an excess of POPE, you can (either manually, or by using a script) randomly choose some POPE to be converted to (or replaced with) POPG by some clever means. This is not a trivial task. Is there a way to multiply the membrane by a _non-integer_ number AND somehow conserve the ratio of different lipid species too? The output is dependent upon the configuration of the input and the box size, so no, there is no straightforward, automatic, way of doing so given the constraints of your box dimensions. Or at the very least, to have both upper and lower leaflets identical after multiplication? (This, too, would help immensely). If you can construct a satisfactory monolayer, you can manipulate its coordinates (i.e. horizontal flip and translation) to create a bilayer. You would have to do plenty of equilibration after doing so, of course. -Justin Thanks, -Shay ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: [gmx-developers] Fwd: Simulating Gases with GROMACS 4.0
This message is better discussed on the gmx-users list, since it is not pertinent to development. I have CC'ed gmx-users@gromacs.org, and further discussion belongs there. PRADEEP VENKATARAMAN wrote: -- Forwarded message -- From: *PRADEEP VENKATARAMAN* pvtul...@gmail.com mailto:pvtul...@gmail.com Date: Tue, Jun 2, 2009 at 5:37 PM Subject: Simulating Gases with GROMACS 4.0 To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Hi I am trying to simulate all atom methane gas (no solvent) at 1 bar and 300 K. I minimized 300 methane molecules in 25X25X25 ang^3 box. Then I doubt you are in the gas phase. Just because you don't have solvent (i.e., water) does not mean you have a gas. This box is probably too small to properly describe a gaseous system, which is mostly empty space. When I try running at NPT simulation using the following pressure coupling parameters, Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 2.0 compressibility = 9.9e-1 ref_p = 1.0 Posting the rest of your .mdp file is more useful. Snippets like this hide the possibility that you've done something else wrong. I encounter the following error. Please help == Step 16271, time 32.542 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.001545, max 0.019029 (between atoms 556 and 557) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 556560 55.30.1113 0.1072 0.1092 556557 50.90.1114 0.1071 0.1092 --- Program mdrun_mpi, VERSION 4.0.5 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1001) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem This issue is reported frequently in the case of an unstable system, i.e.: http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings http://wiki.gromacs.org/index.php/blowing_up If you want any more useful advice, you'll have to describe: 1. Your parameters (force field) 2. The full .mdp file 3. Your preparation steps (minimization, equilibration) -Justin Thanks, Pradeep ___ gmx-developers mailing list gmx-develop...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-developers Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-requ...@gromacs.org. -- 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] crystals of KCl during simulation
Rebeca García Fandiño wrote:
Thank you very much for your answers. Anyway, if I want to simulate
my protein with Amber, would it be a big problem to combine parameter
from Amber with parameters from OPLS for water and/or ions?
Parameters for water might well be the same. Generally speaking, mixing
forcefields is a bad idea. See
http://wiki.gromacs.org/index.php/Parameterization. You might survive
borrowing an ion, but check the literature thoroughly for any reports of
suitable ions, and/or reconsider your force field choice.
Mark
Date: Tue, 2 Jun 2009 09:51:12 -0300
Subject: Re: [gmx-users] crystals of KCl during simulation
From: mo...@ufscar.br
To: gmx-users@gromacs.org
Hi Rebeca,
the paper David suggests is certainly more complete, I just compared OPLS
and Aqvist's parameters for sodium for the specific case of anionic
micelles. anyway, if want to try the Aqvist's parameters take a look
inside ffoplsaa.atp file (opls_408 for K+).
best regards,
André
Rebeca García Fandiño wrote:
Thank you very much, André. Could you please indicate me how could
I use these parameters in Gromacs? I have not seen them included in
ions.itp and I could not find anything in the manual.
Best wishes,
Rebeca.
I would recommend reading the following paper, even though it only is
about NaCl it compares the properties of four different parameter sets,
and IIRC Åqvist's parameters were not so great.
@Article{ Hess2006c,
author = B. Hess and C. Holm and N. {van der Vegt},
title = Osmotic coefficients of atomistic NaCl (aq) force
fields,
journal = J. Chem. Phys.,
year = 2006,
volume = 124,
pages = 164509,
abstract = Solvated ions are becoming increasingly important
for (bio)molecular simulations. But there are not
much suitable data to validate the
intermediate-range solution structure that ion-water
force fields produce. We compare six selected
combinations of four biomolecular Na-Cl force fields
and four popular water models by means of effective
ion-ion potentials. First we derive an effective
potential at high dilution from simulations of two
ions in explicit water. At higher ionic
concentration multibody effects will become
important. We propose to capture those by employing
a concentration dependent dielectric
permittivity. With the so obtained effective
potentials we then perform implicit solvent
simulations. We demonstrate that our effective
potentials accurately reproduce ion-ion coordination
numbers and the local structure. They allow us
furthermore to calculate osmotic coefficients that
can be directly compared with experimental data. We
show that the osmotic coefficient is a sensitive and
accurate measure for the effective ion-ion
interactions and the intermediate-range structure of
the solution. It is therefore a suitable and useful
quantity for validating and parametrizing atomistic
ion-water force fields. (c) 2006 American Institute
of Physics. 0021-9606
}
Date: Mon, 1 Jun 2009 14:52:35 -0300
Subject: RE: [gmx-users] crystals of KCl during simulation
From: mo...@ufscar.br
To: gmx-users@gromacs.org
Hi Rebeca,
I found out a few years ago that OPLS parameters for Na+ were
inadequate
for my simulations on surfactants aggregation due to the
formation of
stable (and unrealistic) ionic bridges. I got better structures
using
Aqvist's parameters (available in GROMACS), maybe you could try
these
parameters for K+ as well.
please let me know if that works.
best regards,
André
Yes, I use PME.
Date: Mon, 1 Jun 2009 19:34:27 +0200
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] crystals of KCl during simulation
Rebeca García Fandiño wrote:
Thank you very much for your answer. I have read some recent
literature,
and you are right, it is a problem about the parameters for
ions
in
Amber.
I have found this paper:
Parameters of Monovalent Ions in the Amber-99 Forcefield:
Assesment of
Inaccuracies and Proposed Improvements
http://pubs.acs.org/doi/abs/10.1021/jp0765392
There, they simulate nucleic acids using a combination of Amber
and
OPLS sigma and epsilon for the ions. I have tried that in the
case of
my
protein, just changing the ion sigma and epsilon in the
topology
by
those corresponding to OPLS, but I still observe
aggregation for
the
ions.
Would this combination of Amber and OPLS have any kind of
potential
problem during the simulation? Has anybody any idea to avoid
this type
of artefact?
Just checking, do you use PME? (You should...)
Thank you very much in advance,
Rebeca.
To:
Re: [gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories
Oliver Stueker wrote:
On 6/1/09 11:48 PM, Mark Abraham wrote:
Jinyao Wang wrote:
Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
but I am getting the following the fatal error:
Fatal error:
Library file aminoacids.dat not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
How can I solve it?
See
http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation
Mark
The procedure on that Wiki-Page actually works in (from my personal
experience)
only ~90% of the cases:
After I installed Gromacs 4.0.5 on a Cluster in my home-directory, tools like
pdb2gmx kept complaining they couldn't find the topology files, as GMXLIB was
actually not set by GMXRC.
Fortunately adding the line:
export GMXLIB=${GMXDATA}/gromacs/top
just after sourcing GMXRC in my .bashrc, worked for me.
Sigh, indeed, you're right. I've always overridden GMXLIB by hand to
accommodate some of my foibles. GMXRC not setting GMXLIB seems to defeat
the point.
Mark
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[gmx-users] PME on BlueGene
Hi, I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the configuration options from the wiki I have succeeded insofar that I have a working program as long as I don't use PME. I have tried many different variants of fftw - 2.1.5, 3.2.1, single precision, double precision, different compiler optimizations and so on, but it all ends the same: mdrun getting stuck somewhere in the initialization process. However, by using the built in fft library FFTPACK instead of FFTW, PME will work, but that is not really an alternative. In at least a few cases I have been able to pinpoint the location where it hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls MPI_Sendrecv, but then nothing else happens as far as I can tell. I'm confused and I have sort of ran out of ideas right now. Has anyone else encountered a problem like this, or has anyone any suggestions how to proceed from here? Thanks, Jakob Wohlert ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PME on BlueGene
Jakob Wohlert wrote: Hi, I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the configuration options from the wiki I have succeeded insofar that I have a working program as long as I don't use PME. I have tried many different variants of fftw - 2.1.5, 3.2.1, single precision, double precision, different compiler optimizations and so on, but it all ends the same: mdrun getting stuck somewhere in the initialization process. However, by using the built in fft library FFTPACK instead of FFTW, PME will work, but that is not really an alternative. In at least a few cases I have been able to pinpoint the location where it hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls MPI_Sendrecv, but then nothing else happens as far as I can tell. I'm confused and I have sort of ran out of ideas right now. Has anyone else encountered a problem like this, or has anyone any suggestions how to proceed from here? That looks to me like the separate PME nodes are dying through some linking problem and the problem is only manifest on node 0 when its sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when all the nodes die at the first point they refer to a symbol in the FFT library. Otherwise, looking at warnings/errors from the linker will be required. Are you compiling an FFT library version for the back end, or the front end? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] PME on BlueGene
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Tuesday, June 02, 2009 7:55 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PME on BlueGene Jakob Wohlert wrote: Hi, I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the configuration options from the wiki I have succeeded insofar that I have a working program as long as I don't use PME. I have tried many different variants of fftw - 2.1.5, 3.2.1, single precision, double precision, different compiler optimizations and so on, but it all ends the same: mdrun getting stuck somewhere in the initialization process. However, by using the built in fft library FFTPACK instead of FFTW, PME will work, but that is not really an alternative. In at least a few cases I have been able to pinpoint the location where it hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls MPI_Sendrecv, but then nothing else happens as far as I can tell. I'm confused and I have sort of ran out of ideas right now. Has anyone else encountered a problem like this, or has anyone any suggestions how to proceed from here? That looks to me like the separate PME nodes are dying through some linking problem and the problem is only manifest on node 0 when its sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when all the nodes die at the first point they refer to a symbol in the FFT library. Otherwise, looking at warnings/errors from the linker will be required. Are you compiling an FFT library version for the back end, or the front end? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in equilibration step
Dear all, I am doing simulation of membrane protein for this I am following justin's tutorial In the first equilibration step i am getting error like this- --- Program mdrun, VERSION 4.0.3 Source code file: trnio.c, line: 252 File input/output error: Cannot write trajectory frame; maybe you are out of quota? Can anyone have idea to solve this problem? If have please let me know. My command line like this- mdrun -v -s nvt.tpr -o new_seq-nvt.trr -c new_seq-nvt.gro -e newe_seq-nvt.edr -g new_seq-nvt.log. My nvt.mdp file is below- title = NVT equilibration for TAP-DMPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 25000 ; 2 * 25000 = 50 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrai ned lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1 ; short-range neighborlist cutoff (in nm) rcoulomb= 1 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cut-off ; coulombtype cut-off pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein DMPC SOL_NA+ ; three coupling groups - more accurat e tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Thanks a lot in advance. Nitu sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in equilibration step
nitu sharma wrote: Dear all, I am doing simulation of membrane protein for this I am following justin's tutorial In the first equilibration step i am getting error like this- --- Program mdrun, VERSION 4.0.3 Source code file: trnio.c, line: 252 File input/output error: Cannot write trajectory frame; maybe you are out of quota? So did you check how much disk space you have left? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem in fianl step of MD
Hi .. I am using gromacs 4.0 for simulating a protein molecule. i am getting following problem during md run[md.mdp dt =0.002 ; ps ! nsteps = 10 ; total 200.0 ps ] t = 47.530 ps: Water molecule starting at atom 46763 can not be settled. Check for bad contacts and/or reduce the timestep. What should i have to do ? please help me.. Rituraj ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem in fianl step of MD
rituraj purohit wrote: Hi .. I am using gromacs 4.0 for simulating a protein molecule. i am getting following problem during md run[md.mdp dt =0.002 ; ps ! nsteps = 10 ; total 200.0 ps ] t = 47.530 ps: Water molecule starting at atom 46763 can not be settled. Check for bad contacts and/or reduce the timestep. What should i have to do ? please help me.. Upgrade to a recent release of GROMACS, and check out http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
