[gmx-users] MDRUN warning during minimization

Justin Lemkul jalemkul at vt.edu
Wed Jan 27 13:43:11 CET 2016 


On 1/26/16 9:31 PM, Agnivo Gosai wrote:
> Hi,
>
> I checked the link provided by Dr. Justin.
>
> The below mentioned lines are from the help in that link:
>
> "There can be a number of reasons for the large velocities in your system.
> If it happens at the beginning of the simulation, your system might be not
> equilibrated well enough (e.g. it contains some bad contacts). Try
> a(nother) round of energy minimization
> <http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation> to
> fix this. Otherwise you might have a very high temperature, and/or a
> timestep <http://www.gromacs.org/Documentation/Terminology/Timestep> that
> is too large. Experiment with these parameters until the error stops
> occurring. If this doesn't help, check the validity of the parameters in
> yourtopology
> <http://www.gromacs.org/Documentation/File_Formats/Topology_File>!"
>
> After the 1st minimization the warning went away as I did not see such a
> thing during the 2nd minimization. To run the 1st minimization I used
> maxwarn -1. Then I did 1 ns of position restrained NVT , 5 ns of position
> restrained NPT and 5 ns of unrestrained MD in the NPT ensemble. There were
> no further warnings.
>

Why are you using -maxwarn 1?  Warnings generally indicate significant problems 
and overriding them is generally a very bad idea.

> However, I see a problem on visualizing the system at each step. This is
> how the system looks at the start of the EM run.
>
> ​
>   simustart.png
> <https://drive.google.com/file/d/0B-U8uULVZjfRS1hpM0xWNGhhdTA/view?usp=drive_web>
> ​ A red colored 6 carbon phenol molecule is present inside the protein.
>
> However after the 1st EM the phenol group is seen to come outside of the
> protein , vibrates about the mean position during the position restrained
> MD  and floats around during the unrestrained MD.
>
> This is the system at the end of EM no 1 with maxwarn -1 in grompp. It can
> be seen that the red colored phenol molecule has come outside.
>
> ​
>   emend.png
> <https://drive.google.com/file/d/0B-U8uULVZjfROVR1eFdHOWlEalU/view?usp=drive_web>
> ​
>  From my trailing mail it may be seen that particles 800 to 807 are
> mentioned in the warning message. Looking at the input topology for grompp
> during EM run I found that these belong to the ligand molecule whose
> parameters were determined using ACPYPE and Antechamber 14. Could this be a
> reason as it may be generating unphysical parameters ?
>
> The protein had all standard residues and I created the topology using
> AMBER99SB. ACPYPE also generated a .top file for each of the ligand and the
> phenol , which I did not use. There is a line in that like this :
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.8333
>
> I am using the .itp files for the ligand and phenol which has the following
> info :
>
> [moleculetype]
> [atom]
> [bond]
>
> etc....
>
> I combined the [ atomtypes ] for those .itp files and copied them in a
> separate file which I mentioned in the GROMACS generated topol.top file
> like this :
>
> ; Include forcefield parameters
> #include "amber99sb.ff/forcefield.itp"
>
> ; Include [atomtypes]
> #include "myligand_atomtypes.itp"
>
> ...............................................................................................................................................
>
>
> So should I look at the parameters for AMBER99SB ?Kindly suggest.
>

Of course.  If your ligand is dissociating (and you know that it shouldn't, 
presumably) then either your .mdp settings are bad (see above about -maxwarn) or 
the ligand topology is bad.  For phenol, it should look a lot like a tyrosine 
side chain, I would imagine.

-Justin

>
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
>
> On Sun, Jan 24, 2016 at 11:16 PM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
>>
>>
>>
>>
>> ---------- Forwarded message ----------
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Cc:
>> Date: Sun, 24 Jan 2016 21:10:17 -0500
>> Subject: Re: [gmx-users] MDRUN warning during minimization
>>
>>
>> On 1/24/16 9:06 PM, Agnivo Gosai wrote:
>>
>>> Dear all,
>>>
>>> I used ACPYPE to create the topology using GAFF for two small molecules
>>> and
>>> then merged everything with the protein topology built using pdb2gmx (
>>> version 4.6.7 and AMBER99SB) and proceeded for simulation.
>>>
>>> At the start of energy minimization this was observed :
>>>
>>> WARNING: Listed nonbonded interaction between particles 800 and 807
>>> at distance 3f which is larger than the table limit 3f nm.
>>>
>>> This is likely either a 1,4 interaction, or a listed interaction inside
>>> a smaller molecule you are decoupling during a free energy calculation.
>>> Since interactions at distances beyond the table cannot be computed,
>>> they are skipped until they are inside the table limit again. You will
>>> only see this message once, even if it occurs for several interactions.
>>>
>>> IMPORTANT: This should not happen in a stable simulation, so there is
>>> probably something wrong with your system. Only change the table-extension
>>> distance in the mdp file if you are really sure that is the reason.
>>>
>>> I am seeing this for the 1st time , kindly help in understanding.
>>>
>>>
>>
>> http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off
>>
>> Google knows lots, too.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

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