[gmx-users] reliability of NOTES

Payman Pirzadeh ppirzade at ucalgary.ca
Wed Jul 22 00:26:52 CEST 2009 

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: 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
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> 

-- 
========================================

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

========================================

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