[gmx-users] Umbrella Sampling gromacs 5.0 error

Alexander Law alexander.law at pg.canterbury.ac.nz
Fri Nov 21 08:39:21 CET 2014


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.

Thanks
Alex
________________________________________
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: Wednesday, November 19, 2014 1:28 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling gromacs 5.0 error

On 11/17/14 11:02 PM, Alexander Law wrote:
> Dear vmx-users
>
> I am running through Dr Lemkul's umbrella sampling tutorial and applying this to my own structure. I have problem with the pull simulation command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
>
> I receive this error message back:
>
>
> Ignoring obsolete mdp entry 'title'
>
> Ignoring obsolete mdp entry 'optimize_fft'
>
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
>
> ERROR: pull-coord1-groups should have 2 components
>
>
> WARNING 1 [file md_pull.mdp, line 62]:
>
>    Unknown left-hand 'pull-group0' in parameter file
>
>
>
>
> WARNING 2 [file md_pull.mdp, line 62]:
>
>    Unknown left-hand 'pull-group1' in parameter file
>
>
>
>
> WARNING 3 [file md_pull.mdp, line 62]:
>
>    Unknown left-hand 'pull_rate1' in parameter file
>
>
>
>
> WARNING 4 [file md_pull.mdp, line 62]:
>
>    Unknown left-hand 'pull_k1' in parameter file
>
>
>
>
> NOTE 2 [file md_pull.mdp]:
>
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>
>    your simulation.
>
>
>
> NOTE 3 [file md_pull.mdp]:
>
>    nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>
>    nstcomm to nstcalcenergy
>
>
>
> NOTE 4 [file md_pull.mdp]:
>
>    leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
>
> ------------------------------
>
> Fatal error:
>
> Group Protein referenced in the .mdp file was not found in the index file.
>
> Group names must match either [moleculetype] names or custom index group
>
> names, in which case you must supply an index file to the '-n' option
>
> of grompp.
>
>
> My Index file is set up properly, with force being applied to Chain_A, and Chain_B is my static reference:
>
> 0 Chain_B             :  1290 atoms
>
> 1 Chain_A             :   110 atoms
>

The fatal error is due to the fact that you've deleted the other necessary
groups.  You should add Chain_A and Chain_B to an index file, but not delete the
other groups.

>
> The md_pull.mdp remains the same:
>
>
> ; Pull code
>
> pull            = umbrella
>
> pull_geometry   = distance  ; simple distance increase
>
> pull_dim        = N N Y
>
> pull_start      = yes       ; define initial COM distance > 0
>
> pull_ngroups    = 1
>
> pull_group0     = Chain_B
>
> pull_group1     = Chain_A
>
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
>
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
>
> Any advice on how to treat this problem is appreciated.
>

Regarding the .mdp keywords, note from the first page of the tutorial:

"PLEASE NOTE: This tutorial has NOT been updated to reflect the new selection
syntax and .mdp options introduced in GROMACS 5.0."

Use an older version (4.6.x) or check the manual for the new syntax; it doesn't
differ much.  I just haven't had the chance to make the changes and verify that
things still work as expected.

-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

==================================================
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
This email may be confidential and subject to legal privilege, it may
not reflect the views of the University of Canterbury, and it is not
guaranteed to be virus free. If you are not an intended recipient,
please notify the sender immediately and erase all copies of the message
and any attachments.

Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more
information.


More information about the gromacs.org_gmx-users mailing list