[gmx-users] Re: Re: Failed Energy Minimization

Justin M. Shorb shorb at wisc.edu
Fri Apr 20 16:34:50 CEST 2007


Thanks for the rapid reply. I have made minor modifications to the 
ffG43a1 force field (the one giving me these errors), but they are 
really considerably minor. I have added an Azide molecule to the rtp 
file (and corresponding atoms to the atp, etc.) and I have also added 
an NME (similar to the NME in the charmm force field).

I decided to go ahead and untar the original 3.3 distribution, and go 
back to the original ffG43a1 force field. This still did not solve the 
problem. In fact, my small molecule is diglycine. If I run it with 
neutral termini, I managed to get it to run through em, after simply 
changing the box of water size (from 1.2 nm to 1.0 nm). This leads me 
to believe it is a problem with the solvation. In fact, often times the 
waters that exhibit infinite force are in the bulk (not even close to 
the solute). This happens if I keep it solvated in spc, or change it to 

The molecule is run through pdb2gmx_d with the following options: 0 
(ffG43a1) -ter 0 (NH3+) 0 (COO-). With those options for a simple 
diglycine, genbox_d should be able to solvate it fine. Also, pdb2gmx_d 
shouldn't have trouble making a top file, either. From inspecting the 
topology file, it looks perfectly fine. (two glycine residues, correct 
atoms and types, good charges, includes all the correct itp files).

Finally, yes: the infinite force always occurs in step 0 with grid 

My shell script only requires an initial pdb file to run, I can send it 
along if it would help diagnose whether or not my version of gmx is 
running correctly. (It is an unmodified source code, so it should be). 
I just am unsure of what else could possibly be going wrong.

Thanks in advance,

> Message: 6
> Date: Fri, 20 Apr 2007 10:19:31 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Failed Energy Minimization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <46280713.2000904 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Justin M. Shorb wrote:
>> Greetings:
>> I have been having trouble running any energy minimization with any 
>> sort
>> of system. I have small polypeptides in water, and then large proteins
>> in water with the same error message:
>> No matter what run parameters I get, I always get ci = -2147483648. 
>> Even
>> different systems. (This, I realize is simply numerically infinity). 
>> If
>> I try running with ns_type = simple, the em runs until it hits around 
>> 35
>> and then says it didn't converge. Since I am running grompp_d -v, I 
>> get
>> that there are certain atoms that have infinite potential. But,
>> depending on the system, the atom type (solvent or molecule) changes.
> This suggests a problem with your force field and/or topology.
>> I have noted that previous posts have been answered with an 
>> admonition:
>> "Find out which atoms are infinite force, and then fix it." I suppose 
>> I
>> could go through, find the atoms and remove those waters that overlap,
>> but shouldn't this be taken into account by the genbox_d program? I 
>> also
>> have tried to increase the vdw radii in the vdwradii.dat file to have 
>> it
>> delete more waters. But, even after having 60 fewer waters around a 88
>> kD protein, the system still fails to energy minimize.
> This suggests that the source of the problem isn't that these atoms
> start life too close together, but maybe they're moving too close
> together because of some other problem? (Unless the error is always
> happening before the first EM step)
>> Given that this seems to be a common problem in solvating a system, 
>> are
>> there better options (options for genbox??) than running the following
>> shell commands? The em.mdp file is also shown below.
> That all seems fine.
> Mark
Justin M. Shorb			Phone: (608) 262-0483
Skinner Group				shorb at wisc.edu
University of Wisconsin-Madison,  Department of Chemistry
1101 University Ave., Madison, WI, 53706

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