[gmx-users] Fattal error in npt_umbrella : Umbrella Sampling Simulations tutorial
Justin Lemkul
jalemkul at vt.edu
Sat Feb 6 18:50:02 CET 2016
On 2/5/16 7:12 PM, Alexander Alexander wrote:
> Thank you for your response.
>
> To solve the problem I just turned of the velocity generation by
> "gen_vel = no" and then it worked fine with Parrinello-Rahman method,
> do you think no side effect it can bring to the work?
>
>
> Here is what showed up in the screen with Parrinello-Rahman method.
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> gmx grompp -f npt_umbrella.mdp -c conf400.gro -p topol.top -n index.ndx
> -o npt400.tpr
>
>
> NOTE 1 [file npt_umbrella.mdp, line 66]:
> npt_umbrella.mdp did not specify a value for the .mdp option
> "cutoff-scheme". Probably it was first intended for use with GROMACS
> before 4.6. In 4.6, the Verlet scheme was introduced, but the group
> scheme was still the default. The default is now the Verlet scheme, so
> you will observe different behaviour.
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'optimize_fft'
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.42#
>
> NOTE 2 [file npt_umbrella.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 npt_umbrella.mdp]:
> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
> nstcomm to nstcalcenergy
>
>
> NOTE 4 [file npt_umbrella.mdp]:
> leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
>
> 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.
>
> Setting the LD random seed to 1659631040
> Generated 165 of the 1596 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
> Excluding 3 bonded neighbours molecule type 'Protein_chain_D'
> Excluding 3 bonded neighbours molecule type 'Protein_chain_E'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'NA'
> Excluding 1 bonded neighbours molecule type 'CL'
> Setting gen_seed to 1801145467
> Velocities were taken from a Maxwell distribution at 310 K
> Removing all charge groups because cutoff-scheme=Verlet
> The center of mass of the position restraint coord's is 3.264 2.151 2.973
> The center of mass of the position restraint coord's is 3.264 2.151 2.973
> Pull group 1 'Chain_A' has 226 atoms
> Pull group 2 'Chain_B' has 226 atoms
> Number of degrees of freedom in T-Coupling group Protein is 2254.90
> Number of degrees of freedom in T-Coupling group non-Protein is 64203.10
> Pull group natoms pbc atom distance at start reference at t=0
> 1 226 113
> 2 226 339 4.324 nm 4.324 nm
> Estimate for the relative computational load of the PME mesh part: 0.10
>
> There were 4 notes
>
> There was 1 warning
>
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1-rc1
> Source code file:
> /home/xxx/gromacs-5.1-rc1/src/gromacs/gmxpreprocess/grompp.c, line: 2101
>
> Fatal error:
> Too many warnings (1), gmx terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> And Below is the screen out of berendsen coupling method
> ++++++++++++++++++++++++++++++++++++++++++++++
> gmx grompp -f npt_umbrella.mdp -c conf400.gro -p topol.top -n index.ndx
> -o npt400.tpr
>
>
> NOTE 1 [file npt_umbrella.mdp, line 66]:
> npt_umbrella.mdp did not specify a value for the .mdp option
> "cutoff-scheme". Probably it was first intended for use with GROMACS
> before 4.6. In 4.6, the Verlet scheme was introduced, but the group
> scheme was still the default. The default is now the Verlet scheme, so
> you will observe different behaviour.
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'optimize_fft'
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.43#
>
> NOTE 2 [file npt_umbrella.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 npt_umbrella.mdp]:
> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
> nstcomm to nstcalcenergy
>
>
> NOTE 4 [file npt_umbrella.mdp]:
> leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
>
> WARNING 1 [file npt_umbrella.mdp]:
> Using Berendsen pressure coupling invalidates the true ensemble for the
> thermostat
>
> Setting the LD random seed to 35424197
> Generated 165 of the 1596 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_D'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_E'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning all bonds into constraints...
> Setting gen_seed to 3254256618
> Velocities were taken from a Maxwell distribution at 310 K
> Removing all charge groups because cutoff-scheme=Verlet
> The center of mass of the position restraint coord's is 3.264 2.151 2.973
> The center of mass of the position restraint coord's is 3.264 2.151 2.973
> Pull group 1 'Chain_A' has 226 atoms
> Pull group 2 'Chain_B' has 226 atoms
> Number of degrees of freedom in T-Coupling group Protein is 2254.90
> Number of degrees of freedom in T-Coupling group non-Protein is 64203.10
> Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
> Calculated rlist for 1x1 atom pair-list as 1.409 nm, buffer size 0.009 nm
> Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
> Note that mdrun will redetermine rlist based on the actual pair-list setup
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 56x40x100, spacing 0.117 0.109 0.120
> Pull group natoms pbc atom distance at start reference at t=0
> 1 226 113
> 2 226 339 4.324 nm 4.324 nm
> Estimate for the relative computational load of the PME mesh part: 0.10
> This run will generate roughly 17 Mb of data
>
> There were 4 notes
>
> There was 1 warning
>
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1-rc1
> Source code file:
> /home/xxxx/gromacs-5.1-rc1/src/gromacs/gmxpreprocess/grompp.c, line: 2101
>
> Fatal error:
> Too many warnings (1), gmx terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
Try V-rescale instead. We should probably change our warning message about
Parrinello-Rahman if we're going to elevate the use of the Berendsen method to
"warning" rather than "note."
-Justin
>
> Best regards,
>
> Alex
>
> On Sat, Feb 6, 2016 at 12:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/5/16 2:50 PM, Alexander Alexander wrote:
>>
>>> Dear Gromacs user,
>>>
>>> I am trying to do the Umbrella simulation following exactly the the
>>> tutorial, everything is fine but I a fatal error happens in .tpr file
>>> generation of npt_umbrella section warning about Pcoupl in
>>> npt_umbrella.mdp
>>> file.
>>> I used the suggested .mdp file in tutorial with Parrinello-Rahman pressure
>>> coupling, but it complained that this type of coupling make the
>>> equilibration unstable, and use Berendsen pressure coupling instead.
>>> Then, I did, but again Fatal error by an warning stating that Berendsen
>>> invalidates the true ensemble for the thermostat.
>>>
>>>
>> Use of the Berendsen weak coupling should not trigger a fatal error. It
>> should produce a note for the user. Can you provide the exact output from
>> the screen, copied and pasted?
>>
>> All the inputs and even the name are fully identical with the tutorial
>>> samples.
>>> The version of Gromacs is : VERSION 5.1-rc1
>>>
>>>
>> Don't use release candidates for production work :) Get the newest
>> version (5.1.2).
>>
>> -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
>>
>> ==================================================
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--
==================================================
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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