[gmx-users] MDRUN warning during minimization

Wed Jan 27 03:31:54 CET 2016

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.

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.

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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