[gmx-users] A jump in potential just after extension
Faezeh Pousaneh
fpoosaneh at gmail.com
Wed Mar 18 09:18:25 CET 2015
Dear Justin,
I use gromacs/4.6.7. <http://4.6.0.7/> Below is my .mdp file. No that is
not similar to my case, I do not change any setting for the extension. (I
should add that despite strange jump in potential in g_energy, the
trajectory goes in a direction which I expect.)
************************************PRODUCTIOn************************************************
integrator = md
dt = 0.002
nsteps = 50000000
nstxout = 10000 ; save coordinates every ps
nstvout = 10000 ; save velocities every ps
nstlog = 10000 ; update log file every
nstenergy = 10000 ; save energies every
nstxtcout = 100000 ; Output frequency for xtc file
xtc-precision = 100000 ; precision for xtc file
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; fs
pbc = xyz ; 3-D PBC
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in
nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
vdw-type = Cut-off
Tcoupl = v-rescale ; modified Berendsen thermostat
tc-grps = LUT SOL ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 380. 380. ; reference
temperature, one for each group, in K
;tc-grps = system
energygrps = LUT SOL
Pcoupl = Parrinello-Rahman
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = no
gen_temp = 380.0
gen_seed = 712349
DispCorr = EnerPres ; account for cut-off vdW
scheme
constraints = all-bonds ; all bonds constrained (fixed
length)
continuation = yes ; Restarting after NPT
constraint-algorithm = lincs ; holonomic constraints
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
**************************************************************************************************************
Best regards
Dear Justin,
>
> I use gromacs/4.6.7. Below is my .mdp file. No that is not similar to my
> case, I do not change any setting for the extension. (I should add that
> despite strange jump in potential in g_energy, the trajectory goes in a
> direction which I expect.)
>
>
> ************************************PRODUCTIOn************************************************
> integrator = md
> dt = 0.002
> nsteps = 50000000
> nstxout = 10000 ; save coordinates every ps
> nstvout = 10000 ; save velocities every ps
> nstlog = 10000 ; update log file every
> nstenergy = 10000 ; save energies every
> nstxtcout = 100000 ; Output frequency for xtc file
> xtc-precision = 100000 ; precision for xtc file
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; fs
> pbc = xyz ; 3-D PBC
> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in
> nm)
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> coulombtype = PME ; Particle Mesh Ewald for
> long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> vdw-type = Cut-off
> Tcoupl = v-rescale ; modified Berendsen
> thermostat
> tc-grps = LUT SOL ; two coupling groups -
> more accurate
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 380. 380. ; reference
> temperature, one for each group, in K
> ;tc-grps = system
> energygrps = LUT SOL
> Pcoupl = Parrinello-Rahman
> Pcoupltype = Isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> gen_vel = no
> gen_temp = 380.0
> gen_seed = 712349
> DispCorr = EnerPres ; account for cut-off vdW
> scheme
> constraints = all-bonds ; all bonds constrained (fixed
> length)
> continuation = yes ; Restarting after NPT
> constraint-algorithm = lincs ; holonomic constraints
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
>
> **************************************************************************************************************
>
>
> Best regards
>
>
> On Mon, Mar 16, 2015 at 12:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/16/15 4:45 AM, Faezeh Pousaneh wrote:
>>
>>> Hi,
>>>
>>> I am almost new in Gromacs, I searched about my problem but did not
>>> find anything. Can someone please help me?
>>>
>>> I extend my simulation with same node on same machine, but when I check
>>> g_energy I find a sharp jump in potential, why is that so?. (for
>>> example if before
>>> the extension the average value of potential were X, just as soon as
>>> extension starts the average jumps to Y.)
>>>
>>> my run command:
>>>
>>> aprun -n 1 tpbconv_mpi -s production.tpr -extend 100000 -o
>>> production.tpr
>>> aprun -n 224 mdrun_mpi -s production.tpr -cpi state.cpt -c
>>> production.gro
>>>
>>>
>> Please post the contents of your original .mdp file. This issue has come
>> up before in very specific cases. Which version of GROMACS are you using?
>>
>> Is it related to http://redmine.gromacs.org/issues/1640 ?
>>
>> -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
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>
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