-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of David van der Spoel Sent: July 15, 2009 2:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote: > Hi, > I tested TIP4P and SPC-E. I used the .gro files in /share/top of the > gromacs. The outputs of energy are: > > TIP4P, 1ns npT, T=300K > > Energy Average RMSD Fluct. Drift > Tot-Drift > ---------------------------------------------------------------------------- > --- > Potential -20929 115.164 113.745 0.0624384 > 62.4385 > Kinetic En. 3781.5 72.9061 72.4712 0.0275462 > 27.5462 > Total Energy -17147.5 98.1701 94.671 0.0899847 > 89.9848 > Temperature 299.906 5.78209 5.7476 0.00218465 > 2.18465 > Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000371707) > > > SPC-E, npT, T= 300K > > Energy Average RMSD Fluct. Drift > Tot-Drift > ---------------------------------------------------------------------------- > --- > Potential -24058.6 114.598 109.211 0.120286 > 120.287 > Kinetic En. 3848.77 73.862 73.7792 -0.0121097 > -12.1097 > Total Energy -20209.9 95.4042 90.1487 0.108177 > 108.177 > > The potential energies are again half of what they should be! Exactly the > same problem with my own six-site model. Initially I thought I might have > done sth in my .itp file, but now, I really do not understand where the > problem comes from!!!! If these boxes contain 512 molecules that means the energy is -42 kJ/mol for TIP4P and slightly lower for SPC/E. Exactly correct. However the distribution contains boxes with 216 molecules, which makes that this is way too low, it should be -9000 for TIP4P. How many molecules do you have? Based on the topology files, I have 515 molecules for SPCE and 506 for TIP4P. have 515 molecules for SPCE and 506 for TIP4P. > > Payman > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of David van der Spoel > Sent: July 15, 2009 12:23 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > Payman Pirzadeh wrote: >> 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? >> > No, only the relaxation rate (with Berendsen scaling) resp. the > oscillation period with Parrinello Rahman. > >> 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 > > -- David. ________________________________________________________________________ David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [email protected] [email protected] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ 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? Read http://www.gromacs.org/mailing_lists/users.php
