Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw.
Payman -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > 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? > Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin > 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 > > -- ======================================== 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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