Hi, I am trying to study the dissolution of urea in water. After adding the water molecule using genbox, I did the energy minimization by applying pbc. Then I run the equilibration for 300ps using NPT anisotropic pressure coulpling and variable axis only in the z direction. The reference pressure is 1 bar. After the run, the cystal structure is deformed (which should n't be).
The mdlog file shows the avg pressure in the range of 2-4e+2 bar. I have attached my parameter file , please help me to find the solution for my problem. Regards, Shankari -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Tuesday, January 16, 2007 1:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] infinitive force acting on atom during Sivashangari Gnanasambandam wrote: > Dear all, > > I run the NPT (anisotropic) for the urea-water system. After the md > run the pressure is not closer to 1 bar but in terms of 100. Suggest > me the corrections in my parameter file. When you post to this list, please use a Subject for your email that is relevant - please do not just reply to the last email you received and change the topic. That way you stand a chance of someone who knows about your problem reading it. This isn't a helpdesk and we aren't obliged to help you, so you stand the best chance of being helped if you make life simple for us. Further, you'll need to provide a lot more information about what you're trying to do in order for us to suggest where you might be wrong, in the same way that ringing up a car mechanic and saying "my 1996 Toyota Camry doesn't work" doesn't get you very far.... For a start, how did you equilibrate this system? How long did you then run it for? Over how long did you collect your statistics for calculating this pressure? Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
minim2.mdp
Description: minim2.mdp
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
