[gmx-users] Re: reliability of NOTES
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 22 00:44:53 CEST 2009
Payman Pirzadeh wrote:
> 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).
Very reliable - the statistical ensemble from the Berendsen thermostat does not
correspond to any known ensemble. This has been well-documented in the
literature for years.
T-coupling choices are listed in the manual:
http://manual.gromacs.org/current/online/mdp_opt.html#tc
Note that V-rescale is one of them :)
> Also, when I changed the thermostat to nose-hoover, it said that it can not
> be used with Berendsen barostat. Why?
I can't recall having read anything about this in particular, but it's probably
somewhere in the literature as well. Use the Parrinello-Rahman barostat instead.
-Justin
>
> Payman
>
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> 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: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>> 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: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org]
>>> 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: gmx-users-bounces at gromacs.org
>> [mailto:gmx-users-bounces at gromacs.org]
>>>> 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: gmx-users-bounces at gromacs.org
>>> [mailto:gmx-users-bounces at gromacs.org]
>>>>> 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: gmx-users-bounces at gromacs.org
>>>> [mailto:gmx-users-bounces at gromacs.org]
>>>>>> 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: gmx-users-bounces at gromacs.org
>>>>> [mailto:gmx-users-bounces at gromacs.org]
>>>>>>> On Behalf Of Payman Pirzadeh
>>>>>>> Sent: July 15, 2009 10:14 AM
>>>>>>> To: jalemkul at vt.edu; '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: gmx-users-bounces at gromacs.org
>>>>> [mailto:gmx-users-bounces at gromacs.org]
>>>>>>> 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: gmx-users-bounces at gromacs.org
>>>>>> [mailto:gmx-users-bounces at gromacs.org]
>>>>>>>> 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: gmx-users-bounces at gromacs.org
>>>>>>> [mailto:gmx-users-bounces at gromacs.org]
>>>>>>>>> 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 gmx-users at gromacs.org
>>>>>>>>>> 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 gmx-users-request at gromacs.org.
>>>>>>>>>> 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
========================================
More information about the gromacs.org_gmx-users
mailing list