Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set?
Payman -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Hi again, > I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in > the [atoms ]are specifies as opls_???, doesn't grompp check the database > for the corresponding parameters? Or we should again manually specify the [ > atomtypes ] again in either .itp or .top file? > You need to #include "ffoplsaa.itp" to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin > Payman > > -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of Payman Pirzadeh > Sent: July 15, 2009 10:14 AM > To: [email protected]; 'Discussion list for GROMACS users' > Subject: RE: [gmx-users] making a box of water > > OK! > I changed my .top file to > > ;This is simulation for TIP4P water model > [ defaults ] > ; non-bondedtype combrule genpairs FudgeLJ > FudgeQQ N > 1 2 NO > > ; include TIP4P topology > #include "tip4p.itp" > > [ system ] > Pure box of water > > [ molecules ] > SOL 506 > > But I still get the same error message! Should I include the [defaults] in > the .itp file? > > Payman > > -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of Justin A. Lemkul > Sent: July 14, 2009 7:56 PM > To: Gromacs Users' List > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> Will #include "ffgmx.itp" solve my problem? Would it be a general solution >> or in each case I should specify (if I add other solutes such as > proteins)? > > Well, ffgmx is deprecated, so it is probably not the best choice :) > Choosing a > force field should not be a haphazard occasion, it is a very important > choice. > For water models, parameters should be uniform, but if you're simulating a > protein, you'll want to make a very educated decision. > > -Justin > >> Payman >> >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] >> On Behalf Of Justin A. Lemkul >> Sent: July 14, 2009 7:07 PM >> To: Gromacs Users' List >> Subject: Re: [gmx-users] making a box of water >> >> >> You need to #include an appropriate force field that contains the >> [defaults], >> [atomtypes], etc. before you can define a [moleculetype]. >> >> -Justin >> >> Payman Pirzadeh wrote: >>> Here is my .top file: >>> >>> ;This includes SPC-E potential >>> #include "spce.itp" >>> >>> [ system ] >>> Pure box of water >>> >>> [ molecules ] >>> SOL 515 >>> >>> I used the same thing with my own model, but it had worked. >>> >>> Payman >>> >>> -----Original Message----- >>> From: [email protected] > [mailto:[email protected]] >>> On Behalf Of Justin A. Lemkul >>> Sent: July 14, 2009 6:54 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] making a box of water >>> >>> >>> >>> Payman Pirzadeh wrote: >>>> Hello, >>>> >>>> I am trying to make a box of water from three different water models. I >>>> can make one from my own water model, but when I want to test TIP4P and >>>> SPCE, as soon as it comes to energy minimization step and using grompp, >>>> I get the following error message: >>>> >>>> >>>> >>>> Program grompp, VERSION 4.0.4 >>>> >>>> Source code file: topio.c, line: 415 >>>> >>>> >>>> >>>> Fatal error: >>>> >>>> Syntax error - File spce.itp, line 1 >>>> >>>> Last line read: >>>> >>>> '[ moleculetype ]' >>>> >>>> Invalid order for directive moleculetype >>>> >>>> >>>> >>>> What is the problem causing the code referring to itp file? >>>> >>> See the message I just sent. Something is out of order in your .top > file. >>> -Justin >>> >>>> Regards, >>>> >>>> >>>> >>>> Payman >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> gmx-users mailing list [email protected] >>>> http://lists.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 > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list [email protected] http://lists.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 list [email protected] http://lists.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? 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