[gmx-users] Umbrella Sampling Error in Gromacs 5.0

[Justin Lemkul]

On 4/22/15 4:59 PM, Jianhui Tian wrote:
>>
>> Date: Wed, 22 Apr 2015 16:05:18 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0
>> Message-ID: <5537FEFE.6020300 at vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 4/22/15 3:54 PM, Jianhui Tian wrote:
>>> Dear Users,
>>>
>>> I am trying to do a umbrella pulling of one lipid out of a bilayer using
>>> umbrella sampling code. In Gromacs 5.0, there is a big change in umbrella
>>> sampling implementation. I set my pull parameters like this:
>>>
>>> pull             = umbrella
>>> pull_geometry   = cylinder  ; Pull in the direction of pull-vec.
>>> pull_coord1_vec = 0.0 0.0 -1.0
>>> pull_r1 = 1.0
>>> pull_r0 = 1.5
>>> pull_start = yes
>>> pull_ngroups = 2
>>> pull_ncoords = 1
>>> pull_coord1_groups     = 1 2
>>> pull_group1_name     = PullLipid  ; one lipid that I want to pull out
>>> pull_group2_name        = RefLipids   ; lipids on the other leaflet of
>>> bilayer
>>> pull_coord1_rate = 0.001 ; 0.001 nm per ps = 1 nm per ns
>>> pull_coord1_k         = 1000      ; kJ mol^-1 nm^-2
>>>
>>> When I have a small system, it can work but had and following error and
>>> stopped:
>>>
>>> Fatal error:
>>> Distance between pull groups 1 and 2 (2.707004 nm) is larger than 0.49
>>> times the box size (2.758373).
>>> You might want to consider using "pull-geometry = direction-periodic"
>>> instead.
>>>
>>> I guess this is due to a small box size (about 5.52 nm in x and y).
>>>
>>> Then I double the system size and redo the umbrella sampling. I got the
>>> following message with grompp:
>>> ########################################################
>>> Pull group  natoms  pbc atom  distance at start     reference at t=0
>>>          1       130     23335
>>>          2      3136     38129    -nan    -nan
>>> ########################################################
>>
>> Something is messed up in the input coordinates.  If the reference
>> distance is
>> "not a number," then you need to diagnose what it is you've done to the
>> coordinates before doing anything else.
>>
>> -Justin
>>
>
> Thanks, Justin.
>
> But, what do you mean by coordinates messed up?

No idea, but you should never see "nan" if everything is sensible.  There are a 
bunch of possibilities, but the ones I can think of would cause a fatal error.

> I have a gro file for generating the tpr for umbrella pulling.
> The same GRO file can be used to generate a tpr file for normal MD run
> without any problems.
>

OK, so it's specific to something being interpreted by the pull code.  Try 
varying some settings to see if it illuminates anything.  Otherwise, you need to 
upload all of your files somewhere (as well as a list of all your commands, 
exactly as you gave them) for us to look into it.

-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

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