[gmx-users] nstlist with vdw only
Would't this mean, that molecules could suddenly appear and lead to a discontinuity in the LJ-potential? Or in what way should I modify the r_vdw according to what rlist? I wanna end with a cut-off of the LJ-potentail around 1.75nm. Thanks in advance Nicolas Erik Lindahl wrote: Hi Nicholas, nstlist=1 means you recalculate the neighborlist every single step, which will be quite expensive. Depending on the type of system and temperature you are simulation you probably want to start somewhere around nstlist=10. Cheers, Erik On Aug 20, 2007, at 10:26 PM, Nicolas Schmidt wrote: Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation-time is used for ns-pairs, only 30-35% for LJ. Am I doing something wrong here? How can this be done more efficient. Thanks to everyone posted the .top and .mdp file along with my output-file -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kanns mit allen: http://www.gmx.net/de/go/multimessenger___ 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 thewww 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] nstlist with vdw only
Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation-time is used for ns-pairs, only 30-35% for LJ. Am I doing something wrong here? How can this be done more efficient. Thanks to everyone posted the .top and .mdp file along with my output-file -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kanns mit allen: http://www.gmx.net/de/go/multimessenger gmx_ethane_0365_32768.e74269 Description: Binary data ethane.itp Description: Binary data ethane_32768.top Description: Binary data md.mdp Description: application/mdp ___ 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] how to build up fixed connections? how to simulate no electrostatics?
(a) Nope, my .mdp-file don't reads that. So I think I don't use one. (b) I use some different software, that does exactly what I want. It's very reliable and it's telling me that the pressure of a 2CLJ-fluid with all the set parameters should be different. Since I wanna do the exact same thing, the higher pressure kind of points out that in fact I'm not doing the same. (c) Exactly! Bondtype 5 doesen't imply a length parameter. So therefor I'm using a constraint. David told me to do so. I'm really unsure at this point, this is why I posted my issue. Still: Though I thought I don't have to specify the electrostatics-section since my molecule doesn't have any charges (or does it???), what to do to totally switch the electrostatics off? Thanks to everyone. David Mobley wrote: Maybe this is naive, but: (a) Are you using pressure regulation? (If so, with which barostat?) (b) How do you know what you expect the pressure to be? (c) By "fixed connections", do you mean fixed bond lengths? Are you doing this using constraints? David On 8/13/07, Nicolas Schmidt <[EMAIL PROTECTED]> wrote: Hey everybody. I'm still trying to biuld up a bulk of 2CLJ-molecules (ethane). I just wanna use fixed connections in-between the CH3-"atoms" and no eletrostatics during the simulation. I posted my .itp-file several times along my .top-file and my used .mdp-file. Though the simulation runs fine I'm unhappy with the results, cause pressure is higher than I expect it to be. Since Mark told me, I'm not simulating fixed connections I'd like to ask if ANYBODY could help me with that. Thanks in advance Nicolas -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail ___ 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 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] how to build up fixed connections? how to simulate no electrostatics?
Hey everybody.
I'm still trying to biuld up a bulk of 2CLJ-molecules (ethane). I just wanna
use fixed connections in-between the CH3-"atoms" and no eletrostatics during
the simulation. I posted my .itp-file several times along my .top-file and my
used .mdp-file. Though the simulation runs fine I'm unhappy with the results,
cause pressure is higher than I expect it to be.
Since Mark told me, I'm not simulating fixed connections I'd like to ask if
ANYBODY could help me with that.
Thanks in advance
Nicolas
--
GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS.
Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail
[ moleculetype ]
; name nrexcl
ethane 1
[ atoms ]
; nrtype resnr residuatomcgnr charge
1 CH3 1 ETH ET1 1 0.000
2 CH3 1 ETH ET2 2 0.000
[ bonds ]
; aiaj funct
1 2 5
[ constraints ]
; i j type lenght
1 2 1 0.2345
;
Preprocessing---
title= Energy Minimization ; redundant,so whatever
comes to your mind
cpp = /usr/bin/cpp ; your preprocessor
;include = /usr/local/gromacs/share/gromacs/top ; directories
to include in your topology
;define = ; for defines in your topology file
;
; Run
Control-
integrator = md ; what you wanna do. md
(moleculardynamics),steep (energyminimization), sd, md, cg, l-bfgs, nm, tpi,...
tinit= 0 ; starting time for your run
dt = 0.00333 ; time step for the integration
nsteps = 3 ; maximum number of steps to integrate
;init_step=; the starting step {t=tinit +dt*(init_step
+i)}
comm_mode= None; removal of center of mass movement
;nstcomm =; frequency of that removal
;comm_grps=; what groups are considered for removal
;
; Langevin
Dynamics---
;bd_fric =; brownian dynamics friction coefficient
;ld_seed =; used to initialize random generator for
thermal noise for stochastic and Brownian dynamics
;
; Energy
Minimization-
;emtol= 1 ; the minimization is converged when the
maximum force is smaller than this value
;emstep = 0.01 ; initial step-size
;nstcgsteep =; frequency of performing 1 steepest descent
step while doing conjugate gradient energy minimization
;nbfgscorr=; Number of correction steps to use for L-BFGS
minimization. A higher number is more accurate, but slower
;
; Shell Molecular
Dynamics
;emtol=; the minimization is converged when the maximum
force is smaller than this value. shell-md: < 1 , em < 10
;niter=; maximum number of iterations for optimizing
the shell positions and the flexible constraints
;fcstep =; the step size for optimizing the flexible
constraints
;
; Output
Control--
nstxout = 1; frequency to write coordinates to output
trajectory file, the last coordinates are always written
nstvout = 1; frequency to write velocities to output
trajectory, the last velocities are always written
;nstfout = ; frequency to write forces to output
trajectory
;nstlog = 5000; frequency to write energies to log file,
the last energies are always written
;nstenergy= 250 ; frequency to write energies to energy
file, the last energies are always written
;nstxtcout= 250 ; frequency to write coordinates to xtc
trajectory
;xtc_percision= ; precision to write to xtc trajectory
;xtc_grps = Protein ; group(s) to write to xtc trajectory,
default the whole system is written (if nstxtcout is larger than zero)
;energygrps = Protein SOL ; group(s) to write to energy file
;
; Neighbor
Searching
[gmx-users] Re: doing simplest simulations
>> Second: Am I simulating fixed connections? >No I once wrote in a mail in may I think: >> This may be a really simple question, I know, but still... >> >> How can I set up a fixed connection between two atoms of a molecule? When I >> choose the 5th bondtype in my topology-file I get the following output from >> grompp (though it's processing, so I CAN start mdrun afterwards): >> >> WARNING 1 [file "ethane.itp", line 12]: >> No default Connect Bonds types, using zeros >> >> Either way I'm not sure how the distance of these two atoms is processed, so >> there is NO parameter that is specifying this bond-type (and a constraint >> would be processed by gromacs, wouldn't it? And I don't want it to, cause I >> want the simulation to be as simple as possible) >> >> By the way, I wanna simulate a huge system of ethane and take a look at the >> processing time per simulated step, is there an output-file thats reading >> this? >> >> Thanks in advance to everyone who is replying, it's so hard when you're >> stuck. >[ constraint ] >; i j type length >1 2 1 0.15 > >-- >David. So what's my mistake? I posted my .itp-file, do I have to do a change in the forcefield-files? When 'yes', what change? ;-) >> Are my chosen options on the .mdp-file therefor correct? >By comparison with what? To build up a fixed connection. What therefor to choose in the bonds section of the .mdp-file? constraints = none, all??? Is in the Electrostatics-section of the .mdp-file >coulombtype = cut-off >rcoulomb = 0 sufficient to not simulate any electrostatics? If not, what else should I do? ;-) to Mark: thanks for your help, it's definitely not in the way that I'm refusing to take your advice 'bout the tutorials, but it's sometimes uneasy to find out some kind of an exception from the rule (fixed connections, no electrostatics, prefering speed to accuracy, and so on). Why doing an energy minimization when I equilibrate at an higher temperature and cool down afterwards? And of course I'm a newbie, otherwise I'd answer questions and not ask them. and most of all, I just have to do ONE set of simulations (with an various amount of molecules) to compare gromacs' speed in simulating large systems of simple gas molecules. I wanna do well, otherwise I'd just take what I got from the already finished simulations. But afterwards I'm done and won't bother you again. ;-) Thanks again. Nicolas posted the most recent .mdp-file and .itp-file as well. -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail md.mdp Description: application/mdp OneEthane.itp Description: Binary data ___ 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] doing simplest simulations
Hi again, I re-did my simulations with the posted .mdp-file. The huge differences to my formerly posted file are a few vanished semicolons, and after a fine simulation-run an added dispersion correction due to a pressure that was slightly higher than expected. Did't really help, made it worse. But at least the simulations are now at the speed I expected them to be (gromacs doesen't scale that beautiful under my configuration, any suggestions???). Anyhow, two further questions: First: Is the configuration with r_list = r_vdw and nst_list = 1 a good choice, especially regarding speed? Suggestions? (I caught a glimpse at the archives of this forum and couldn't quite find out why the radius of the neighbour-list has to be smaller than r_vdw, isn't that list something similar to the verlet-neighbour-lists? Shouldn't it therefore be bigger? But in this case I'm just curious...) Second: Am I simulating fixed connections? Are my chosen options on the .mdp-file therefor correct? Is gromacs doing as less as possible? Got sometimes at simulations with higher density complains 'bout constraints. Have I chosen the right configuration in the .itp-file? to Mark: Nope, no warnings, posted this time the output-file as well. But I can't write bigger gro-files (gromacs'complaining something like "can't allocate memory"). But this isn't a that big problem for me, 125000 molecules are sufficient. I wanna simulate as fast as possible with only reasonable results, so I'm unsure why I should use anymore options. I'm T-coupling at 183K cause I want my bulk at this temperature. No more reason. And by doing so (along the annealing) I'm simulating a nucleation-process. Works fine for me. Considering the missing equilibration: My first posted file missed the vanished semicolons at the annealing, posted not the most recent file, my bad, sorry. The simulation-results still were rubbish. And now they are more or less fine (slightly higher pressure, 5.9 instead of 4.6 bar), of course I'm only measuring at the end of my siimulation run. Changed the thermostat and r_list, so maybe that was the problem. Thanks anyway and in advance Nicolas Mark wrote: Nicolas Schmidt wrote: Hi, I'm doing a comparison in the aspect of speed between gromacs and an other MD-simulation-program, that isn't providing all the diffrent options of gromacs. My problem is, that the results I got from the simulations with gromacs aren't reasonable. E.g negative pressure and zero kelvin or ridiculously high pressure and temperature. The simulations are running more or less fine (though they are too fast ;-) ), but if the results are rubbish I can't say anything 'bout the speed at all... I'm assuming your protocol sets up a system of bulk ethane with a reasonable density, and that there were no warnings you overlooked. Of course I'm assuming I did a terribly stupid mistake, so I'm asking you to take a look at my files (added all necessary ones) and correct me (they are less big than you might emagine, resulting from the pretty simple molecules I'm buidling up) Energy minimization before beginning equilibration MD is usually a good idea. I've no idea why you think turning off basically the entire set of .mdp options is a good idea, or why you're T-coupling at 183K. Since you're new, I'd check out http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and follow along some tutorial material, and then adapt a protocol and .mdp file to your needs. Trying to measure temperature and pressure from a single run that didn't have a pre-equilibration phase is just asking for a crazy result. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Gromacs Runs One Microsecond At Cannonball Speeds 2 1ETHET11 0.769 0.769 0.744 1ETHET22 0.769 0.769 0.794 1.53748 1.53748 1.53748 #include "ffgmx.itp" #include "OneEthane.itp" [ system ] ;Name pure ethane [ molecules ] ;Compound #mols ethane 64000 NNODES=16, MYRANK=0, HOSTNAME=noco013.nec NNODES=16, MYRANK=1, HOSTNAME=noco013.nec NNODES=16, MYRANK=2, HOSTNAME=noco042.nec NNODES=16, MYRANK=3, HOSTNAME=noco042.nec NNODES=16, MYRANK=5, HOSTNAME=noco066.nec NNODES=16, MYRANK=4, HOSTNAME=noco066.nec NNODES=16, MYRANK=6, HOSTNAME=noco067.nec NNODES=16, MYRANK=7, HOSTNAME=noco067.nec NNODES=16, MYRANK=8, HOSTNAME=noco068.nec NNODES=16, MYRANK=9, HOSTNAME=noco068.nec NNODES=16, MYRANK=11, HOS
[gmx-users] doing simplest simulations
Hi, I'm doing a comparison in the aspect of speed between gromacs and an other MD-simulation-program, that isn't providing all the diffrent options of gromacs. My problem is, that the results I got from the simulations with gromacs aren't reasonable. E.g negative pressure and zero kelvin or ridiculously high pressure and temperature. The simulations are running more or less fine (though they are too fast ;-) ), but if the results are rubbish I can't say anything 'bout the speed at all... Of course I'm assuming I did a terribly stupid mistake, so I'm asking you to take a look at my files (added all necessary ones) and correct me (they are less big than you might emagine, resulting from the pretty simple molecules I'm buidling up) Thanks in advance Nicolas ___ 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] add to "doing simplest simulations
Sorry 'bout that, this time with the files...
Gromacs Runs One Microsecond At Cannonball Speeds
2
1ETHET11 0.769 0.769 0.744
1ETHET22 0.769 0.769 0.794
1.53748 1.53748 1.53748
#include "ffgmx.itp"
#include "OneEthane.itp"
[ system ]
;Name
pure ethane
[ molecules ]
;Compound #mols
ethane 125000
;
Preprocessing---
title= Energy Minimization ; redundant,so whatever
comes to your mind
cpp = /usr/bin/cpp ; your preprocessor
;include = /usr/local/gromacs/share/gromacs/top ; directories
to include in your topology
;define = ; for defines in your topology file
;
; Run
Control-
integrator = md ; what you wanna do. md
(moleculardynamics),steep (energyminimization), sd, md, cg, l-bfgs, nm, tpi,...
tinit= 0 ; starting time for your run
dt = 0.00333 ; time step for the integration
nsteps = 3 ; maximum number of steps to integrate
;init_step=; the starting step {t=tinit +dt*(init_step
+i)}
comm_mode= None; removal of center of mass movement
;nstcomm =; frequency of that removal
;comm_grps=; what groups are considered for removal
;
; Langevin
Dynamics---
;bd_fric =; brownian dynamics friction coefficient
;ld_seed =; used to initialize random generator for
thermal noise for stochastic and Brownian dynamics
;
; Energy
Minimization-
;emtol= 1 ; the minimization is converged when the
maximum force is smaller than this value
;emstep = 0.01 ; initial step-size
;nstcgsteep =; frequency of performing 1 steepest descent
step while doing conjugate gradient energy minimization
;nbfgscorr=; Number of correction steps to use for L-BFGS
minimization. A higher number is more accurate, but slower
;
; Shell Molecular
Dynamics
;emtol=; the minimization is converged when the maximum
force is smaller than this value. shell-md: < 1 , em < 10
;niter=; maximum number of iterations for optimizing
the shell positions and the flexible constraints
;fcstep =; the step size for optimizing the flexible
constraints
;
; Output
Control--
nstxout = 1; frequency to write coordinates to output
trajectory file, the last coordinates are always written
nstvout = 1; frequency to write velocities to output
trajectory, the last velocities are always written
;nstfout = ; frequency to write forces to output
trajectory
;nstlog = 5000; frequency to write energies to log file,
the last energies are always written
;nstenergy= 250 ; frequency to write energies to energy
file, the last energies are always written
;nstxtcout= 250 ; frequency to write coordinates to xtc
trajectory
;xtc_percision= ; precision to write to xtc trajectory
;xtc_grps = Protein ; group(s) to write to xtc trajectory,
default the whole system is written (if nstxtcout is larger than zero)
;energygrps = Protein SOL ; group(s) to write to energy file
;
; Neighbor
Searching--
nstlist = 5 ; Frequency to update the neighbor list. When
this is 0, the neighbor list is made only once
ns_type = grid ; grid or simple (grid for large systems)
pbc = xyz ; periodic boundary conditions, xyz (every
direction), no (no pbc)
rlist= 1.75 ; cut-off distance for the short-range
neighbor list
;
;
Electrostatics--
;coulombtype = cut-off ; other: Ew
[gmx-users] seriell but parallel ???
Dear gromacs-users, First of all thanks to all contributers of the answers considering my first issue, actually this was my first simulation on gromacs, so maybe this explains my kind of unnecessary questions ;-) Anyway, again a probably easy to solve problem: I only got the possibility to run all the gromacs programs on a single processor engine, in addition to that I have access to a unix cluster (206 x 2 Intel Xeon 3.2 GHz), where ONLY mdrun_mpi was installed. It's in heavy use, so I can't just try if something works, I have to wait a day or two, till I can find out, if a simulation worked or not. I read in the manual, that I would have to use the same amount of nodes (option -np of mdrun_mpi) as I typed in at grompp, but this option doesn't exist in my version of grompp installed on an serial computer. So my question is: Is this a problem? In the case of an existing problem, is there any possibility to solve it, without installing anything on the cluster? Thanks in advance to everyone contributing. and just to everybody: Have a nice weekend. -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail ___ 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] bondtype 5
This may be a really simple question, I know, but still... How can I set up a fixed connection between two atoms of a molecule? When I choose the 5th bondtype in my topology-file I get the following output from grompp (though it's processing, so I CAN start mdrun afterwards): WARNING 1 [file "ethane.itp", line 12]: No default Connect Bonds types, using zeroes Either way I'm not sure how the distance of these two atoms is processed, so there is NO parameter that is specifying this bond-type (and a constraint would be processed by gromacs, wouldn't it? And I don't want it to, cause I want the simulation to be as simple as possible) By the way, I wanna simulate a huge system of ethane and take a look at the processing time per simulated step, is there an output-file thats reading this? Thanks in advance to everyone who is replying, it's so hard when you're stuck. -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail ___ 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
