[gmx-users] Umbrella Sampling gromacs 5.0 error

Alexander Law alexander.law at pg.canterbury.ac.nz
Mon Nov 24 00:39:30 CET 2014

Hi Justin 

I downloaded the compressed folder from this website: http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Computing_potentials_of_mean_force%3A_Justin_Lemkul,_Session_2A

Within it the the npt_umbrella.mdp file reads continuation = yes, gen-vel = yes.

I've ran ~15 simulations over the weekend with continuation = yes, gen-vel= no

Are these simulations unsuitable for umbrella sampling?

I am assuming they are, so I've started a new sequence with not_umbrella.mdp reading the same as: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp
This produces this error:
 WARNING 1 [file npt_umbrella.mdp]:
  You are generating velocities so I am assuming you are equilibrating a
  system. You are using Parrinello-Rahman pressure coupling, but this can
  be unstable for equilibration. If your system crashes, try equilibrating
  first with Berendsen pressure coupling. If you are not equilibrating the
  system, you can probably ignore this warning.

Since I am not equilibrating I've avoided this using the -maxwarn command and started a new sequence for umbrella sampling.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Saturday, November 22, 2014 1:29 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling gromacs 5.0 error

On 11/21/14 7:26 AM, Justin Lemkul wrote:
> On 11/20/14 7:52 PM, Alexander Law wrote:
>> Hi Justin
>> Thank you for taking the time and helping me out. I am now using the 4.6.5
>> version to avoid this sort of error, however I have come across another error
>> which I am not too sure about, it is at the start of the umbrella sampling
>> section of your tutorial, after allocating which frames are to analysed during
>> umbrella sampling. The error reads:
>> ERROR 1 [file npt_umbrella.mdp]:
>>    Generating velocities is inconsistent with attempting to continue a
>>    previous run. Choose only one of gen-vel = yes and continuation = yes.
>> This is after the command: grompp -f npt_umbrella.mdp -c conf1.gro -p
>> topol.top -n index.ndx -o npt1.tpr
>> I am assuming that it is better to delete the continuation command and let the
>> pull coding take place, as I have not changed the amount of force being
>> applied in the Z axis and therefore should be identical to the previous
>> simulation (at frame 1, at frame 100, the chain will be shifted). But I am
>> unsure which one should be omitted.
> The "continuation" keyword indicates whether or not constraints have already
> been solved, which they have in this case, but it's really irrelevant.  The
> easiest thing to do is just set gen_vel = yes to start a new run.  I thought I
> had corrected this long ago, but apparently not.

The file provided in the tutorial should not trigger this error; it has
"continuation = no" and "gen_vel = yes," which is consistent with starting a new
run.  I don't know how the error could have been triggered unless you have
modified the file.



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

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