[gmx-users] Re: local pressure v4.5 issues

[Jianguo Li]

How large is the number? Does the large number converges? Lateral pressure is 
usually large (positive or negative) at the water-hydrophobic interface. e.g., 
see figures in this paper: J. Am. Chem. Soc. 2011, 133, 3720–3723.

Cheers,
Jianguo





________________________________
From: Amit Choubey <kgp.amit at gmail.com>
To: Jianguo Li <ljggmx at yahoo.com.sg>; Discussion list for GROMACS users 
<gmx-users at gromacs.org>
Sent: Wednesday, 22 June 2011 00:16:43
Subject: Re: [gmx-users] Re: local pressure v4.5 issues




On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:

Hi Amit,
>
>May I ask you a question? 
>In your calculation of local pressure using a trajectory file, did you get a 
>single averaged localpressure.dat file? Or else you get a bunch of separate 
>files for each frame (e.g., localpressure.dat0, localpressure.dat1, 
>localpressure.dat2 ....)?
>

Yes I do get different files for different trajectories. All the files seem to 
have the same problem ie a very large/small number printed as tensor elements of 
the pressure for some of the voxels.

Do you have such problems ? Could we compare our methodologies to use the local 
pressure version ?

Amit

>Thank you very much!
>
>Cheers,
>Jianguo
>
>
>
>
>
________________________________
From: Amit Choubey <kgp.amit at gmail.com>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Sent: Monday, 20 June 2011 07:08:03
>Subject: [gmx-users] Re: local pressure v4.5 issues
>
>
>Dear all,
>
>
>I did another simulation with only SPC water. Then I used the local pressure 
>gromacs to calculate the stresses. It seems to be reasonable. 
>
>
>I am not sure how to figure out what goes wrong with my previous simulations 
>when plugged into the local pressure gromacs.
>
>
>Could someone help me in figuring out whats the issue ?
>
>
>Thank You.
>
>
>On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey <kgp.amit at gmail.com> wrote:
>
>Dear all,
>>
>>I installed the git version of local pressure calculation from 
>>
>>http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
>>
>>The I invoked mdrun
>>
>>mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1
>>
>>This created a file named "localpressure.dat0". This is a binary file so I could 
>>not look at it directly. I am not sure if there is a tool in the gromacs to look 
>>at it directly. 
>>
>>
>>To look at the data in "localpressure.dat0" I used the planar_av.c code 
>>available in "pressure-tools" folder at
>>
>>http://md.chem.rug.nl/cgmartini/index.php/3d
>>
>>When I look at the Pressure tensor averaged over xy plane, some of the numbers 
>>are reasonable but few of them are ridiculously large numbers which is not 
>>expected. 
>>
>>
>>I checked this on two different simulations and I got the same problems. The 
>>simulations had run OK previously.
>>
>>Could someone help me in figuring our whats going on ?
>>
>>Amit Choubey
>>
>>
>
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