[gmx-users] solvent except water
Hi what command and what option apply solvent except water in MD simulation by gromacs. Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] solvent except water
leila karami wrote: Hi what command and what option apply solvent except water in MD simulation by gromacs. Any help will highly appreciated! WHat do you mean? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] solvent except water
Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] solvent except water
leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] solvent except water
Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] solvent except water
rasoul nasiri wrote: Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? You can use genbox with mixed solvents. I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] solvent except water
David van der Spoel wrote: rasoul nasiri wrote: Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? You can use genbox with mixed solvents. There are even how-to's on the Gromacs site to accomplish this: http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto: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 MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Scaling of Coordinates is Occurring - why?
From what I can find, it seems that you are correct to assume that frozen coordinates should not be scaled: http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html and, from the online manual: freezegrps: Groups that are to be frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. Lipid SOL). freezedim specifies for which dimension the freezing applies. To avoid spurious contibrutions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time. Note that frozen coordinates are not subject to pressure scaling. Nevertheless, you say that your frozen coordinates are subject to pressure scaling. I can suggest the following: 1. Are you really freezing what you think you are freezing? I see no freeze info in your post so I can't check for myself. i.e. do you have proper freezegrps? did you utilize freezedim? did you include energygrp_excl (which, although required, shouldn't affect frozen atom scaling if you forgot it). Note that your refcoord_scaling only matters if you are using position restraints, which you say you are not. 2. Just use position restraints with a large force constant and use that refcoord_scaling = no. 3. If you're absolutely sure, file a bugzilla. -- original message -- Pressure coupling is not supposed to scale the coordinates of my frozen group, yet it is. My frozen group is a crystal structure that does not have any topology assigned to them: no bond, angle, dihedral constants etc. specified. I find that a crystal structure gets compressed. A sample of the pressure coupling section of my .mdp file is given below: ; PRESSURE COUPLING pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 50.0 compressibility = 0.1 0.1 0.1 0.1 0.1 0.1 refcoord_scaling = no ref_p = 1000.0 1000.0 1000.0 0.0 0.0 0.0 I'm using Gromacs 4.0.5. Any suggestions appreciated, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Scaling of Coordinates is Occurring - why?
chris.ne...@utoronto.ca wrote: From what I can find, it seems that you are correct to assume that frozen coordinates should not be scaled: http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html and, from the online manual: freezegrps: Groups that are to be frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. Lipid SOL). freezedim specifies for which dimension the freezing applies. To avoid spurious contibrutions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time. Note that frozen coordinates are not subject to pressure scaling. Nevertheless, you say that your frozen coordinates are subject to pressure scaling. I can suggest the following: 1. Are you really freezing what you think you are freezing? I see no freeze info in your post so I can't check for myself. i.e. do you have proper freezegrps? did you utilize freezedim? did you include energygrp_excl (which, although required, shouldn't affect frozen atom scaling if you forgot it). Note that your refcoord_scaling only matters if you are using position restraints, which you say you are not. 2. Just use position restraints with a large force constant and use that refcoord_scaling = no. 3. If you're absolutely sure, file a bugzilla. This is a known problem. The options freezing and pressure coupling are not compatible. Ref_coordscaling refers to position restraints, see http://manual.gromacs.org/current/online/mdp_opt.html#pc There is no general solution for this, since pressure scaling may make the box so small that the frozen system is larger than the box (the same problem holds for position restraints by the way). We would like to do this rigorously but as far as I know no-one has worked out a solution. It gets more complicated when constraints are involved. -- original message -- Pressure coupling is not supposed to scale the coordinates of my frozen group, yet it is. My frozen group is a crystal structure that does not have any topology assigned to them: no bond, angle, dihedral constants etc. specified. I find that a crystal structure gets compressed. A sample of the pressure coupling section of my .mdp file is given below: ; PRESSURE COUPLING pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 50.0 compressibility = 0.1 0.1 0.1 0.1 0.1 0.1 refcoord_scaling = no ref_p = 1000.0 1000.0 1000.0 0.0 0.0 0.0 I'm using Gromacs 4.0.5. Any suggestions appreciated, -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: implicit wall doesn't recognize the wall_atomtype correctly?
Hi, Firstly, regarding my last email, even though I didn't get any complain about the nonsense setting for the wall_atomtype from grompp, the mdrun is crashed after some steps. Then I tested some atomtypes which have been given in OPLS, and checked the output in md.log: a) When wall_atomtype = opls_135 in .mdp, *wall_atomtype[0]=2*(wall_atomtype[1]=2) in md.log. b) When wall_atomtype = SI in .mdp, * wall_atomtype[0]=9*(wall_atomtype[1]=9) in md.log. c) When wall_atomtype = opls_1001 in .mdp, *wall_atomtype[0]=9*(wall_atomtype[1]=9) in md.log, where opls_1001 is the atome type for graphene carbon added by myself. Does anyone know about why the md.log give different result from the .mdp file? and what does the *wall_atomtype[0]=2 (or 9)* means? Thanks a lot in advance! best wishes, Baofu Qiao 2010/1/15 Baofu Qiao qia...@gmail.com Hi all, I want to know whether it is a bug or not: When I use some nonsense wall_atomtype for the implicit wall, the grompp doesn't complain about it. Or it is a mistake I make myself. I am using gmx 4.0.7. See the following flags of wall_atomtype. nwall= 2 wall_type= 9-3 wall_r_linpot = 0.1 wall_atomtype= *abc 123;opls_abc opls_abc* wall_density = 144 144 wall_ewald_zfac= 3 best wishes, Baofu Qiao -- Sincerely yours, ** Dr. Baofu Qiao Institute of Computational Physics, University of Stuttgart TEL:+49-711-685 63607 ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The size of the domain decomposition grid (1) does not match the number of nodes (8).
Hello,
I have a run that was working fine under parallel mdrun -pd and when I
then switched to domain decomposition I got:
Fatal error:
The size of the domain decomposition grid (1) does not match the
number of nodes (8). The total number of nodes is 8
while running like this:
/scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -mca
btl_sm_num_fifos 7 -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -mca
btl self,sm -machinefile $PBS_NODEFILE
/scratch/cneale/GPC/exe/intel/gromacs-4.0.5_berkpdfix/exec/bin/mdrun_openmpi
-deffnm md1 -dlb yes -npme -1 -cpt 1 -maxh 47.5 -cpi md1.cpt -px
coord.xvg -pf force.xvg -rdd 2.5
If I then add -dd 2 2 2 to the mdrun command line it runs fine.
I found a couple of things about this on the mailing list but nothing
that seemed entirely related to this case, e.g.:
http://oldwww.gromacs.org/pipermail/gmx-developers/2008-September/002721.html
I'm not sure there's a question here beyond the standard does it seem
as if I forgot to do something?.
Here's the log file:
Log file opened on Sat Jan 16 23:33:54 2010
Host: gpc-f105n032 pid: 24876 nodeid: 0 nnodes: 8
The Gromacs distribution was built Fri Jan 8 20:42:07 EST 2010 by
cne...@gpc-f101n084 (Linux 2.6.18-128.7.1.el5 x86_64)
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) 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 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.
:-)
/scratch/cneale/GPC/exe/intel/gromacs-4.0.5_berkpdfix/exec/bin/mdrun_openmpi
(-:
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 ---
parameters of the run:
integrator = sd
nsteps = 875
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 0
nstxout = 875
nstvout = 875
nstfout = 875
nstenergy= 250
nstxtcout= 250
init_t = 0
delta_t = 0.004
xtcprec = 1000
nkx = 54
nky = 56
nkz = 96
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 = No
epc = Berendsen
epctype = Semiisotropic
tau_p= 4
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):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi
