Hello, I am trying to prepare the input files for an MD run. After running grompp, I received the following note:
NOTE 1 [file npt.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. How reliable this note is? And how can I implement V-rescale thermostat in y input file (I found nothing in the manual). Also, when I changed the thermostat to nose-hoover, it said that it can not be used with Berendsen barostat. Why? Payman -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:38 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > You were right! The dimensions of the box are zero in the .gro file. Should > I change them to the values I have? > As long as those vectors define the box size and not necessarily the system size (i.e., largest coordinate - smallest coordinate). You can do this with a .pdb file, I think on the CRYST line, if you prefer. -Justin > Payman > > -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of Justin A. Lemkul > Sent: July 16, 2009 12:08 PM > To: Gromacs Users' List > Subject: Re: [gmx-users] making a box of water > > > > Payman Pirzadeh wrote: >> But, I am using a .pdb file as the input of the gromacs. Does the >> preparation of pdb file differ from software to software? >> > > It shouldn't, and I'm not 100% sure on how Gromacs handles system size from > a > .pdb file (I always use .gro). What you can try to do is transform your > .pdb > into .gro format with editconf, and read the last line of the .gro file. > That's > any easy way to determine the size of the box Gromacs is finding. > > -Justin > >> Payman >> >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] >> On Behalf Of Justin A. Lemkul >> Sent: July 16, 2009 11:42 AM >> To: Gromacs Users' List >> Subject: Re: [gmx-users] making a box of water >> >> >> >> Payman Pirzadeh wrote: >>> 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. >>> >> Well, Gromacs doesn't do anything in A, it's all nm, so be sure that >> everything >> you're doing is consistent with Gromacs conventions. There is no reason >> that >> either of those boxe should be complaining about a 1.0-nm cutoff, so there >> has >> to be something that messed up along the way. >> >> -Justin >> >>> 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? Read http://www.gromacs.org/mailing_lists/users.php
