Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR:
ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? 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
