[gmx-users] doing simplest simulations

[Nicolas Schmidt]

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 list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ethane_0365.gro
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070810/39ca6cd7/attachment.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ethane_64000.top
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070810/39ca6cd7/attachment-0001.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: gmx_ethane_0365_64000.e73207
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070810/39ca6cd7/attachment-0002.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: md.mdp
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070810/39ca6cd7/attachment-0003.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: OneEthane.gro
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070810/39ca6cd7/attachment-0004.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: OneEthane.itp
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070810/39ca6cd7/attachment-0005.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: orders.txt
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070810/39ca6cd7/attachment.txt>