Re: [gmx-users] Re: Calculate individual force between each atom pair
Hi, On May 20, 2007, at 11:50 PM, WU Yanbin wrote: Thanks for the suggestions. I have traced the calling sequence from do_force() to calculate LJ forces: do_force() --force() --do_nonbonded(). But in do_nonbonded() function of nonbonded.c file, if for general processor, it should have call gmx_nb_generic_kernel() function but this line is in fact commented and the implimentation of gmx_nb_generic_kernel() can not be found. My gromacs version is v3.3. So is there previous implementation of this function? I can write it myself but the efficiency will be much lower. Any suggestions? Thanks in advance. No, the generic loop is actually something new we haven't implemented yet (well, only partly at least). The idea is to have three levels of optimization, depending both on the architecture and how complicated/custom interactions you want to do. 1. For common simulation setups on common hardware you will run the manually tuned assembly kernels. 2. When that isn't possible, we have a wider selection of automatically generated kernels in C/Fortran (the nb_kernel directory). These are somewhat optimized for different hardware when it comes to prefetching, the 1/sqrt(x) calls, but do not use any inline assembly. 3. If you want to do esoteric interactions such as multipoles or hack your own functional form, we intend to have a generic C-language kernel with a switch statement for the type of interaction inside the innermost loop. This is not good for performance, but it should be straightforward both to understand and hack, not to mention it can be faster than using tables for the interactions. For reference, have a look at the 1,4-interactions routine to see what it would look like. Cheers, Erik ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polarizability
Hi, there's a very recent paper of the GROMOS team, where they evaluate the free energy of polarization (with the 'Charge-on-Spring' model): http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html Their code is already working, but under the GROMOS software... Ciao, Patrick Jones de Andrade a écrit : Hi David They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually split into two IIRC, with point dipoles as well as shell models (that means either or). I've found two papers for charmm polariability. But I'll only be able to try to find it in the library or to ask for the authors tomorrow at least. But thanks for the information! ;) On the other hand, I could not yet find any published material from amber using shell models. Is this only an inside group discussion? I think there is not a lot of difference, but shell models are easier to implement. I think too. In reality, there is no visible rational reason for this fear of me, is more like a feeling, so I'll try to find something more on it. But I do agree that it's much likely that the shell model is much easier to implement, if not faster to execute also. :) I am working on shell models a bit (not enough...) Me too. Specially cause this is long terms plans (2+ years from now). But thanks a lot for all information, David. Helped a lot. Sincerally yours, Jones ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] REMD log files
Hi, Thanks for your previous responses to my questions on REMD. I have a general question about understanding REMD in gromacs. Can someone break down how to read the .log file? For instance, one of the main goals I have is to graph the time evolution of temperature exchange for a specific replica (eg. Replica 4). I would like to show that my simulation was able to have a random walk in temperature space. Furthermore, how would I show a random walk in potential energy space? My trouble is that I don't know where to extract this information from an REMD log file. There is one small section from my .log file after an REMD run below for an example. Thanks, Max Replica exchange at step 200 time 0.2 Repl 5 - 6 dE = 4.948e+00 Repl ex 0 1 2 3 4 5 6 7 8 9 x 10 11 x 12 13 14 15 Repl pr .00 .00 .01 .00 1.0 .71 .01 Step Time Lambda 3000.30.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.005681 5 6 0.001385 After LINCS 0.21 54 56 0.07 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 2.09992e+021.44621e+017.48359e+009.96865e+019.55457e+02 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) Coul. recip. 1.02075e+04 -2.66400e+02 -6.36147e+041.24965e+01 -8.58854e+03 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -6.09626e+041.12505e+04 -4.97121e+043.16629e+02 -6.97164e-01 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polarizability
Hi Jones, Charge-on-spring model is another name for shell model. Here's what's written in the introduction of the paper: [...]in the charge-on-spring (or Drude-oscillator or shell) model, an additional point charge is attached to a polarizable center that can adapt its position to the electric field to induce a net dipole.[...] Ciao, Patrick Jones de Andrade a écrit : Hi Patrick. Just got this paper here, thanks for the indication. This may sound like a dumb question, but: am I wrong, or the shell model and the charge on a spring model differ only by the fact that the VdW interation is also floating aroung in the shell model but not in the charge on a spring one? Thanks a lot, Jones On 5/21/07, *Patrick Fuchs* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Hi, there's a very recent paper of the GROMOS team, where they evaluate the free energy of polarization (with the 'Charge-on-Spring' model): http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html Their code is already working, but under the GROMOS software... Ciao, Patrick Jones de Andrade a écrit : Hi David They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually split into two IIRC, with point dipoles as well as shell models (that means either or). I've found two papers for charmm polariability. But I'll only be able to try to find it in the library or to ask for the authors tomorrow at least. But thanks for the information! ;) On the other hand, I could not yet find any published material from amber using shell models. Is this only an inside group discussion? I think there is not a lot of difference, but shell models are easier to implement. I think too. In reality, there is no visible rational reason for this fear of me, is more like a feeling, so I'll try to find something more on it. But I do agree that it's much likely that the shell model is much easier to implement, if not faster to execute also. :) I am working on shell models a bit (not enough...) Me too. Specially cause this is long terms plans (2+ years from now). But thanks a lot for all information, David. Helped a lot. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs
Re: [gmx-users] Testing Gromacs
Kedar Potdar a écrit : Hi all, I could build Gromacs successfully on Linux system and now I would like to test it. So is there a way to test Gromacs? Does the Gromacs package come with basic test suites? I couldn't find anything pertaining to testing on the Gromacs' site. Help in this regard will be highly appreciated. With warm regards, *KEDAR* I've done some benchmarks for our cluster based on the gmxbench, let me know if you are interested in the test set (i've basically created a chained benchmark, one job is launched when the first has finished), but it may be too specific (using LAM/MPI on a sge batch system). Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs-antechamber-gaff
David, On 5/18/07, David van der Spoel [EMAIL PROTECTED] wrote: Francesco Pietra wrote: Planning to use gromacs aided by antechamber/gaff for my recurrent need of new bonded parameters, and having noticed that antechamber's tutorial refers to Sybyl and Gaussian, my question: Is it possible to use a QM suite different from Gaussian? My own suite calculates perfectly RESP and CRESP. Or am I going to loose antechamber's help? I am prone to set manually, atom per atom, RESP or CRESP that I can calculate. Similarly, is it possible to use a non-Sybyl MM package that also imports/saves pdb files? I know that one should come with precise technical questions, though, the above seem inescapable problems/obstacles to me for accessing gromacs. Thanks I haven't used it myself really, but some people have (e.g. Fujitani et al, J. Chem. Phys. 123 084108 (2006)). You can use antechamber to use your nonbonded atoms, but these have to be compatible with the charges. So if you need to use another program than Gaussian, you need to use the recommended level of theory anyway. Since the standard level of theory for GAFF is not extremely high, this should not be a problem. Out of curiosity, which is your own suite? It occurs to me that you may want to add our AMBER-to-GROMACS converter tool to your contributions page (or at least a link to where it resides); I get lots of off-list e-mails asking about it, and I send it out a lot. It's at http://www.alchemistry.org/FreeEnergyTools. Thanks, David -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Strategy for chaining jobs using different mdp parameters (long)
Dear colleagues,
I've done many chained simulations up to now but i'm encoutering
problems and i'm skeptical about some choices i made before. In order to
clear this up, i'd like you to share your experience, so that'll answer
my needs and be a good template for the upcoming wiki.
I want (and need) to chain jobs with different conditions for 3 reasons:
1 - cluster needs (need to split jobs), tpbconv could be sufficient, but
i'm changing parameters
2 - ensemble changing (switching from NVT to NPT for instance)
3 - dynamics fine-control (posre on specific atoms/groups)
Please see below and the attached files for run parameters.
a) NVT then NPT.
I've tried using NVT (pr1) for starting my simulation and then NPT
(pr2). The major differences between pr1 (NVT) and pr2 (NVT) are:
pr1:
Pcoupl = no
gen_vel= yes
---
pr2:
Pcoupl = berendsen
gen_vel= no
The runs are chained like this:
(ini directory contains the top and gro file from previously minimised
structure, mdp directory contains the reference mdp)
pr1 step:
grompp \
-f ../mdp/pr1.mdp \
-p ../ini/molecule_ini.top \
-pp molecule_pr1.top \
-c ../ini/molecule_ini.gro \
-o molecule_pr1.tpr \
-po molecule_pr1.mdp
mdrun \
-s molecule_pr1.tpr \
-o molecule_pr1.trr \
-c molecule_pr1.gro \
-g molecule_pr1.log \
-e molecule_pr1.edr \
-nice 0
pr2 step:
grompp \
-f ../mdp/pr2.mdp \
-p ../ini/molecule_ini.top \
-pp molecule_pr2.top \
-c ../ini/molecule_ini.gro \
-o molecule_pr2.tpr \
-t ../pr1/molecule_pr1.trr \
-po molecule_pr2.mdp
(note there is no -e ../pr1/molecule_pr1.edr since we're switching from
NVT to NPT, as pointed out by Mark Abraham on the list
http://www.gromacs.org/pipermail/gmx-users/2007-May/027193.html)
mdrun \
-s molecule_pr2.tpr \
-o molecule_pr2.trr \
-c molecule_pr2.gro \
-g molecule_pr2.log \
-e molecule_pr2.edr \
-nice 0
As you may have noticed, i'm doing positionnal restraints (pr) runs at
theses steps.
Do i need to specify unconstrained_start= yes?
I've not used it for the moment...
Is there any specific precaution to take while doing this?
In particular, i'm seing for the NPT (pr2) start:
#
Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
-1.59647e+20 -1.59647e+20
Correcting invalid box:
old box (3x3):
old box[0]={-9.82630e+20, 0.0e+00, -0.0e+00}
old box[1]={ 0.0e+00, -8.90833e+20, -0.0e+00}
old box[2]={ 0.0e+00, 0.0e+00, -1.12456e+21}
new box (3x3):
new box[0]={-9.82630e+20, 0.0e+00, -0.0e+00}
new box[1]={ 0.0e+00, -8.90833e+20, -0.0e+00}
new box[2]={ 0.0e+00, 8.90833e+20, -1.12456e+21}
#
Of course the system exploses (but this is another story, in the ml,
David van der Spoel stated this could be due to a system setup problem,
i'll open a new thread on this specific problem).
I'm not completely sure if the problem arises from my specific system or
if i'm missing something while switching from NVT to NPT (see below for
reference files).
b) Reference files while continuing the run (not using tbpconv)
Even if i use the same NPT conditions, i still see some parameters
problem, for instance:
#
Warning: atom names in ../pr1/test_min_deflated25_sol_ions.top and
../pr1/OR1G1_min_formd.gro don't match (OW - HW2)
Warning: atom names in ../pr1/test_min_deflated25_sol_ions.top and
../pr1/OR1G1_min_formd.gro don't match (HW1 - OW)
Warning: atom names in ../pr1/test_min_deflated25_sol_ions.top and
../pr1/OR1G1_min_formd.gro don't match (HW2 - HW1)
Warning: atom names in ../pr1/test_min_deflated25_sol_ions.top and
../pr1/OR1G1_min_formd.gro don't match (OW - HW2)
#
I've understood this comes from the usage of -shuffle *and* -sort option
(and actually, to get the proper ordering, there is only g_desort, as
mentionned in
http://www.gromacs.org/pipermail/gmx-users/2007-January/025584.html),
but i'm suspicious about the -renum and -renumbs options in grompp
(on by default), if it alters the resulting -processed- topology, or not.
To be clear, i'm not completely sure if i need to do:
starting conformation = ../ini/molecule.top and ../ini/molecule.gro
directories :
mkdir {ini,pr1,pr2}
pr1 step:
grompp \
-f ../mdp/pr1.mdp \
-p ../ini/molecule_ini.top \
-pp molecule_pr1.top \
-c ../ini/molecule_ini.gro \
-o molecule_pr1.tpr \
-po molecule_pr1.mdp
mdrun \
-s molecule_pr1.tpr \
-o molecule_pr1.trr \
-c molecule_pr1.gro \
-g molecule_pr1.log \
-e molecule_pr1.edr \
-nice 0
pr2 step:
grompp \
-f ../mdp/pr2.mdp \
-p ../ini/molecule_ini.top \
-pp molecule_pr2.top \
-c ../ini/molecule_ini.gro \
-o molecule_pr2.tpr \
-t ../pr1/molecule_pr1.trr \
-po molecule_pr2.mdp
mdrun \
-s molecule_pr2.tpr \
-o molecule_pr2.trr \
-c molecule_pr2.gro \
-g
[gmx-users] Strange error from my simulation
While switching from NVT to NPT, i'm crashing my simulation.
The error message seen is (repeated 10 times, then mdrun aborts):
#
Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
-1.59647e+20 -1.59647e+20
Correcting invalid box:
old box (3x3):
old box[0]={-9.82630e+20, 0.0e+00, -0.0e+00}
old box[1]={ 0.0e+00, -8.90833e+20, -0.0e+00}
old box[2]={ 0.0e+00, 0.0e+00, -1.12456e+21}
new box (3x3):
new box[0]={-9.82630e+20, 0.0e+00, -0.0e+00}
new box[1]={ 0.0e+00, -8.90833e+20, -0.0e+00}
new box[2]={ 0.0e+00, 8.90833e+20, -1.12456e+21}
.
---
Program mdrun_lam, VERSION 3.3.1
Source code file: ns.c, line: 265
Fatal error:
Box was shifted at least 10 times. Please see log-file.
---
#
I've searched in the archives this could be related to a non
sufficiently equilibrated system, but the first 20ps NVT run fine, so i
presume there's either a problem in the way i'm doing it (thus the
RFC-like question from the other message) or i'm missing something obvious.
Since i've tried to eliminate many errors and still get these errors
after different trials (removing shuffle and sort, generating or not
velocities while switching from pr1 to pr2, i've also tried the
unconstrained_start=yes).
If you have any pointer, i'll be very happy to read it ...
I'm still looking at my setup system (protein in a water/spc solvent) in
order to find where is my error, but since the NVT run seems ok
(analysing precisely it at the moment, but no visual problem neither any
hint in the logs), i'm willing to understand why the switch to NPT fails.
Cheers,
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
title= MD simulation of OR1G1 with full explicit membrane
and solvant
; Preprocessing
cpp = /lib/cpp
define = -DPOSRE
; Run parameters
integrator = md
dt = 0.002
nsteps = 1; 20 ps for PR1
nstcomm1
comm_mode= linear
; File outuput
nstxout = 500
nstvout = 250
nstlog = 250
nstenergy= 250
nstxtcout= 500
; Molecule decomposition
xtc_grps = Protein 478 SOL CL-
energygrps = Protein 478 SOL CL-
nstlist = 5
ns_type = grid
pbc = xyz
rlist= 0.9
; Electrostatics VdW
coulombtype = PME
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = yes ; try to get some time left for long
simulations
rcoulomb = 0.9
rvdw = 1.4
vdwtype = Cut-off
; Temperature
tcoupl = berendsen
tc-grps = Protein 478 SOL CL-
tau_t= 0.1 0.1 0.1 0.1
ref_t= 300 300 300 300
; Pression
Pcoupl = no
Pcoupltype = isotropic
tau_p= 10
ref_p= 1.0
compressibility = 4.5e-5
; Velocities while at 300 K
gen_vel = yes
gen_temp = 300
gen_seed = -1
; Constraints
constraints = all-bonds
constraint_algorithm = lincs
freezegrps = Protein-H 478
freezedim= Y Y Y Y Y Y
title= MD simulation of OR1G1 with full explicit membrane
and solvant
; Preprocessing
cpp = /lib/cpp
define = -DPOSRE
; Run parameters
integrator = md
dt = 0.002
nsteps = 5000 ; 10 ps for PR2
nstcomm1
comm_mode= linear
; File outuput
nstxout = 500
nstvout = 250
nstlog = 250
nstenergy= 250
nstxtcout= 500
; Molecule decomposition
xtc_grps = Protein 478 SOL CL-
energygrps = Protein 478 SOL CL-
nstlist = 5
ns_type = grid
pbc = xyz
rlist= 0.9
; Electrostatics VdW
coulombtype = PME
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = yes ; try to get some time left for long
simulations
rcoulomb = 0.9
rvdw = 1.4
vdwtype = Cut-off
; Temperature
tcoupl =
Re: [gmx-users] gromacs-antechamber-gaff
Sorry to have been the spark for troubles. At any event, one should be aware (if I understand correctly) that to convert from Amber to Gromacs with the alchemistry script below, one should have also the Amber code installed. Should it work at all with Amber 9, instead of the Amber 7 suggested. In conclusion (if I understand) there might be a reason for such conversions if Gromacs code provides serious advantages (parallelization? I see a lot of warnings about this aspect, which with QM codes belongs to the far past) over Amber code. This is not endorsing any choice. I am still at the window (without s). Cheers francesco pietra --- David Mobley [EMAIL PROTECTED] wrote: David, On 5/18/07, David van der Spoel [EMAIL PROTECTED] wrote: Francesco Pietra wrote: Planning to use gromacs aided by antechamber/gaff for my recurrent need of new bonded parameters, and having noticed that antechamber's tutorial refers to Sybyl and Gaussian, my question: Is it possible to use a QM suite different from Gaussian? My own suite calculates perfectly RESP and CRESP. Or am I going to loose antechamber's help? I am prone to set manually, atom per atom, RESP or CRESP that I can calculate. Similarly, is it possible to use a non-Sybyl MM package that also imports/saves pdb files? I know that one should come with precise technical questions, though, the above seem inescapable problems/obstacles to me for accessing gromacs. Thanks I haven't used it myself really, but some people have (e.g. Fujitani et al, J. Chem. Phys. 123 084108 (2006)). You can use antechamber to use your nonbonded atoms, but these have to be compatible with the charges. So if you need to use another program than Gaussian, you need to use the recommended level of theory anyway. Since the standard level of theory for GAFF is not extremely high, this should not be a problem. Out of curiosity, which is your own suite? It occurs to me that you may want to add our AMBER-to-GROMACS converter tool to your contributions page (or at least a link to where it resides); I get lots of off-list e-mails asking about it, and I send it out a lot. It's at http://www.alchemistry.org/FreeEnergyTools. Thanks, David -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=listsid=396545433 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs-antechamber-gaff
Francesco, At any event, one should be aware (if I understand correctly) that to convert from Amber to Gromacs with the alchemistry script below, one should have also the Amber code installed. Should it work at all with Amber 9, instead of the Amber 7 suggested. Yes, this works with AMBER 7, 8, and 9 as far as I know (haven't used with AMBER 7 myself, but have with 8 and 9). And yes, it does require an AMBER installation. Someone is free to generalize it to not depend on AMBER... David In conclusion (if I understand) there might be a reason for such conversions if Gromacs code provides serious advantages (parallelization? I see a lot of warnings about this aspect, which with QM codes belongs to the far past) over Amber code. This is not endorsing any choice. I am still at the window (without s). Cheers francesco pietra --- David Mobley [EMAIL PROTECTED] wrote: David, On 5/18/07, David van der Spoel [EMAIL PROTECTED] wrote: Francesco Pietra wrote: Planning to use gromacs aided by antechamber/gaff for my recurrent need of new bonded parameters, and having noticed that antechamber's tutorial refers to Sybyl and Gaussian, my question: Is it possible to use a QM suite different from Gaussian? My own suite calculates perfectly RESP and CRESP. Or am I going to loose antechamber's help? I am prone to set manually, atom per atom, RESP or CRESP that I can calculate. Similarly, is it possible to use a non-Sybyl MM package that also imports/saves pdb files? I know that one should come with precise technical questions, though, the above seem inescapable problems/obstacles to me for accessing gromacs. Thanks I haven't used it myself really, but some people have (e.g. Fujitani et al, J. Chem. Phys. 123 084108 (2006)). You can use antechamber to use your nonbonded atoms, but these have to be compatible with the charges. So if you need to use another program than Gaussian, you need to use the recommended level of theory anyway. Since the standard level of theory for GAFF is not extremely high, this should not be a problem. Out of curiosity, which is your own suite? It occurs to me that you may want to add our AMBER-to-GROMACS converter tool to your contributions page (or at least a link to where it resides); I get lots of off-list e-mails asking about it, and I send it out a lot. It's at http://www.alchemistry.org/FreeEnergyTools. Thanks, David -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=listsid=396545433 ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strategy for chaining jobs using different mdp parameters (long)
Stéphane Téletchéa wrote:
Dear colleagues,
I've done many chained simulations up to now but i'm encoutering
problems and i'm skeptical about some choices i made before. In order to
clear this up, i'd like you to share your experience, so that'll answer
my needs and be a good template for the upcoming wiki.
I want (and need) to chain jobs with different conditions for 3 reasons:
1 - cluster needs (need to split jobs), tpbconv could be sufficient, but
i'm changing parameters
2 - ensemble changing (switching from NVT to NPT for instance)
3 - dynamics fine-control (posre on specific atoms/groups)
Please see below and the attached files for run parameters.
a) NVT then NPT.
I've tried using NVT (pr1) for starting my simulation and then NPT
(pr2). The major differences between pr1 (NVT) and pr2 (NVT) are:
pr1:
Pcoupl = no
gen_vel= yes
---
pr2:
Pcoupl = berendsen
gen_vel= no
Of course, there's more to it than this, because the non-no choices
activate other options, particularly for pressure coupling.
The runs are chained like this:
(ini directory contains the top and gro file from previously minimised
structure, mdp directory contains the reference mdp)
pr1 step:
grompp \
-f ../mdp/pr1.mdp \
-p ../ini/molecule_ini.top \
-pp molecule_pr1.top \
-c ../ini/molecule_ini.gro \
-o molecule_pr1.tpr \
-po molecule_pr1.mdp
mdrun \
-s molecule_pr1.tpr \
-o molecule_pr1.trr \
-c molecule_pr1.gro \
-g molecule_pr1.log \
-e molecule_pr1.edr \
-nice 0
Do be aware that mdrun -deffnm molecule_pr1 -nice 0 is available to do
this in a much less verbose manner :-)
pr2 step:
grompp \
-f ../mdp/pr2.mdp \
-p ../ini/molecule_ini.top \
-pp molecule_pr2.top \
-c ../ini/molecule_ini.gro \
-o molecule_pr2.tpr \
-t ../pr1/molecule_pr1.trr \
-po molecule_pr2.mdp
(note there is no -e ../pr1/molecule_pr1.edr since we're switching from
NVT to NPT, as pointed out by Mark Abraham on the list
http://www.gromacs.org/pipermail/gmx-users/2007-May/027193.html)
mdrun \
-s molecule_pr2.tpr \
-o molecule_pr2.trr \
-c molecule_pr2.gro \
-g molecule_pr2.log \
-e molecule_pr2.edr \
-nice 0
As you may have noticed, i'm doing positionnal restraints (pr) runs at
theses steps.
Do i need to specify unconstrained_start= yes?
I've not used it for the moment...
There's not a strong need to use it while switching ensembles (in that
you're going to have to re-equilibrate anyway) but I think you should
use it to reduce the occurrence of problems.
Is there any specific precaution to take while doing this?
In particular, i'm seing for the NPT (pr2) start:
#
Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
-1.59647e+20 -1.59647e+20
Correcting invalid box:
old box (3x3):
old box[0]={-9.82630e+20, 0.0e+00, -0.0e+00}
old box[1]={ 0.0e+00, -8.90833e+20, -0.0e+00}
old box[2]={ 0.0e+00, 0.0e+00, -1.12456e+21}
new box (3x3):
new box[0]={-9.82630e+20, 0.0e+00, -0.0e+00}
new box[1]={ 0.0e+00, -8.90833e+20, -0.0e+00}
new box[2]={ 0.0e+00, 8.90833e+20, -1.12456e+21}
#
Of course the system exploses (but this is another story, in the ml,
David van der Spoel stated this could be due to a system setup problem,
i'll open a new thread on this specific problem).
I'm not completely sure if the problem arises from my specific system or
if i'm missing something while switching from NVT to NPT (see below for
reference files).
b) Reference files while continuing the run (not using tbpconv)
Even if i use the same NPT conditions, i still see some parameters
problem, for instance:
#
Warning: atom names in ../pr1/test_min_deflated25_sol_ions.top and
../pr1/OR1G1_min_formd.gro don't match (OW - HW2)
Warning: atom names in ../pr1/test_min_deflated25_sol_ions.top and
../pr1/OR1G1_min_formd.gro don't match (HW1 - OW)
Warning: atom names in ../pr1/test_min_deflated25_sol_ions.top and
../pr1/OR1G1_min_formd.gro don't match (HW2 - HW1)
Warning: atom names in ../pr1/test_min_deflated25_sol_ions.top and
../pr1/OR1G1_min_formd.gro don't match (OW - HW2)
#
I've understood this comes from the usage of -shuffle *and* -sort option
(and actually, to get the proper ordering, there is only g_desort, as
mentionned in
http://www.gromacs.org/pipermail/gmx-users/2007-January/025584.html),
but i'm suspicious about the -renum and -renumbs options in grompp
(on by default), if it alters the resulting -processed- topology, or not.
To be clear, i'm not completely sure if i need to do:
starting conformation = ../ini/molecule.top and ../ini/molecule.gro
directories :
mkdir {ini,pr1,pr2}
pr1 step:
grompp \
-f ../mdp/pr1.mdp \
-p ../ini/molecule_ini.top \
-pp molecule_pr1.top \
-c ../ini/molecule_ini.gro \
-o molecule_pr1.tpr \
-po molecule_pr1.mdp
