[gmx-users] Error while running mdrun with rerun option for LIE calculation
shagun krishna
krishna.shagun123 at gmail.com
Fri Jan 8 18:35:08 CET 2016
Dear Justin,
Thanks a lot. I have successfully completed mdrun with -rerun option. I
have ran the mdrun command on the original mdrun.xtc using new .mdp
settings without PME, and the result was stored in new .edr file. This new
.edr file was then subjected to g_energy to obtain the values of LJ-17 and
Coulomb-14. Hope we have to calculate this only not the LJ-(SR) or
Coulomb-(SR) ?
>>> mdrun -s md_sol_rerun_LLP.tpr (ORIGINAL tpr obtained from Ligand
Simulation in water) -rerun md2_LLP.xtc ( ORIGINAL ,xtc obtained from
Ligand Simulation in water) -x after_rerun_trial4.xtc (OUTPUT) -e
after_rerun_trial4.edr (OUTPUT)
After that I calculated value of Elj and Eqq from g_energy module by
passing these output to g_energy:
>>>> g_energy -f after_rerun_trial4.edr -o after_rerun_trial4_C-14.xvg
>>>>g_energy -f after_rerun_trial4.edr -o after_rerun_trial4_LJ-14.xvg
I got Elj= 271.04 and Eqq=-149.214. Then these values were passed to g_lie
module to get the Delta G for unbound ligand.
>>>> g_lie -f after_rerun_trial4.edr -b 7000 -e 10000 -Elj 271.04 -Eqq
-149.214 -ligand M_R -o lie_ligand.xvg
I am taking last 3000ps of my simulation for calculating energy. Is it good
or should I calculate it from 0 to 10000ps.
After passing these values to g_lie I am getting DGbind = -8.956 (214.311).
In g_lie module we will give the original .edr file or that we have
obtained after rerun. However, I have used the .edr obtained with rerun
option. The values of Clj and Cqq were taken as default (0.181 and 0.5
respectively). I want to know that do we also need to calculate the values
of Clj and Cqq ???
Thanks once again in advance.... :)
Best regards,
Shagun
On Fri, Jan 8, 2016 at 6:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/8/16 12:50 AM, shagun krishna wrote:
>
>> Hiii Justin,
>>
>> Thank you very much for your help. After changing my settings according to
>> your suggestions I am not getting the previous errors. :) The grompp
>> command ran successfully, but when I am evoking the mdrun using rerun
>> option I am getting a fatal error. Please have a look at my terminal
>> window. And let me know how to solve this. What I guess that probably I
>> should increase my box size. My ligand has almost 55 atom.
>>
>>
> You're post-processing an existing system; you can't increase the box size
> and make anything work. The error is related to domain decomposition,
> which you don't need during a rerun anyway, so just do the rerun on a
> single core (or maybe via OpenMP, but I don't know if that works). Just
> avoid MPI, which triggers DD.
>
> -Justin
>
>
> cbb at cbb-Precision-T1700:~/Desktop/md_ligand_RJC02836$ grompp -f
>> md_SOL_rerun.mdp -c equil.gro -o md_sol_rerun.tpr
>> :-) G R O M A C S (-:
>>
>> :-) VERSION 4.6.5 (-:
>>
>> Ignoring obsolete mdp entry 'title'
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
>>
>> NOTE 1 [file md_SOL_rerun.mdp]:
>> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>> nstcomm to nstcalcenergy
>>
>> Generated 168 of the 1653 non-bonded parameter combinations
>> Excluding 3 bonded neighbours molecule type 'M_R'
>> turning all bonds into constraints...
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> turning all bonds into constraints...
>>
>> NOTE 2 [file topol.top]:
>> The largest charge group contains 11 atoms.
>> Since atoms only see each other when the centers of geometry of the
>> charge
>> groups they belong to are within the cut-off distance, too large charge
>> groups can lead to serious cut-off artifacts.
>> For efficiency and accuracy, charge group should consist of a few
>> atoms.
>> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>>
>> Analysing residue names:
>> There are: 1 Other residues
>> There are: 859 Water residues
>> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
>> into groups...
>> Number of degrees of freedom in T-Coupling group M_R is 106.94
>> Number of degrees of freedom in T-Coupling group SOL is 5151.06
>> Largest charge group radii for Van der Waals: 0.370, 0.293 nm
>> Largest charge group radii for Coulomb: 0.370, 0.307 nm
>>
>> NOTE 3 [file md_SOL_rerun.mdp]:
>> The sum of the two largest charge group radii (0.676770) is larger than
>> rlistlong (1.400000) - rcoulomb (0.900000).
>> With exact cut-offs, better performance can be obtained with
>> cutoff-scheme = Verlet, because it does not use charge groups at all.
>>
>> This run will generate roughly 199 Mb of data
>>
>> There were 3 notes
>>
>> Back Off! I just backed up md_sol_rerun.tpr to ./#md_sol_rerun.tpr.2#
>>
>> gcq#139: "We All Get the Flu, We All Get Aids" (LIVE)
>>
>> cbb at cbb-Precision-T1700:~/Desktop/md_ligand_RJC02836$ mdrun -s
>> md_sol_rerun.tpr -rerun md_sol.xtc
>> :-) G R O M A C S (-:
>>
>> Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
>>
>> :-) VERSION 4.6.5 (-:
>>
>> :-) mdrun (-:
>> Back Off! I just backed up md.log to ./#md.log.2#
>> Reading file md_sol_rerun.tpr, VERSION 4.6.5 (single precision)
>> Using 4 MPI threads
>> Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine,
>> which is better)
>>
>> Back Off! I just backed up traj.trr to ./#traj.trr.2#
>>
>> Back Off! I just backed up ener.edr to ./#ener.edr.2#
>> starting md rerun 'M_R in water', reading coordinates from input
>> trajectory
>> 'md_sol.xtc'
>>
>> Reading frame 0 time 0.000
>> WARNING: Some frames do not contain velocities.
>> Ekin, temperature and pressure are incorrect,
>> the virial will be incorrect when constraints are present.
>>
>> Reading frame 140 time 280.000
>> DD cell 0 0 0: Neighboring cells do not have atoms: 45
>>
>> DD cell 2 0 0: Neighboring cells do not have atoms: 32
>>
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.6.5
>> Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/domdec_con.c,
>> line:
>> 722
>>
>> Fatal error:
>> DD cell 0 0 0 could only obtain 11 of the 12 atoms that are connected via
>> constraints from the neighboring cells. This probably means your
>> constraint
>> lengths are too long compared to the domain decomposition cell size.
>> Decrease the number of domain decomposition grid cells or lincs-order.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> Thanks a ton...I am really very thankful to you... :)
>>
>> Best regards,
>>
>> Shagun
>>
>>
> --
> ==================================================
>
> 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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