-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of David van der Spoel Sent: July 15, 2009 2:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote: > -----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. Then it is fine. Which energy do you get for your own model? These are the results I got. It includes all the initial equilibration time during which simulation box got distorted. Energy Average RMSD Fluct. Drift Tot-Drift ---------------------------------------------------------------------------- --- Potential -21955.7 739.133 538.245 -1.7548 -1754.8 Kinetic 4015.45 105.699 98.5134 -0.132693 -132.693 Total -17940.3 775.785 552.229 -1.88749 -1887.49 If I ignore that piece of trajectory, then the average will be 22174.95. But, I can not understand how these values are fine? What is the connection between the values in the tables and the literature values (~-40kJ/mol)? I am truly confused!!! > > > > > > >> 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
