Thanks a lot!!!! That was a big clarification and relief!!!! So, my model is working! Since the RDFs are also correct! Regards,
Payman -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of David van der Spoel Sent: July 15, 2009 2:50 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 2:38 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!!! You have to divide by the number of molecules. g_energy -nmol N > > > >> >> >> >> >> >>> 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
