[gmx-users] Umbrella sampling and PMF calculations

[Justin Lemkul]

On 6/2/17 6:40 PM, Alex wrote:
>>
>> I find that surprising.  Please provide the full, exact error and your
>>> pull settings.  All of the geometries should work with zero or non-zero
>>> pull rates. But I admit, it has been many years since I used GROMACS with
>>> the pull code.
>>>
>>
> Simply take your pull code from the tutorial and replace 'distance' with
> 'direction-periodic' or 'cylinder' (along with some r0/r1). The error is
> that the pull vector cannot be (0 0 0), do not remember the exact text.

A pull vector can indeed not be (0, 0, 0) but that's not a pull rate.

> Setting the pull rate to something like 1e-12 results in the same error.
> Our cluster is down for maintenance until Monday, will give you the exact
> excerpt, if needed.
> 

If you want to troubleshoot further, yes.

-Justin

>>
>>
>>>
>>>
>> Old GROMACS versions had a "position" geometry that was the go-to for
>> membrane/slab/layered systems and worked quite nicely, but that's gone now,
>> replaced by other options that I've never used.
> 
> 
> How old? I have 5.0.4 on another machine here...
> 

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

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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