Hi Justin,
Thanks a lot for your reply. I really appreciate the gromacs_user
folrun help line.
I see! thats why you are not receiving any attachment!
My goal is to compute only GB-energy. I have computed only GB- energy
using Amber and Other packages. Now I am using Gromacs to do the same.
As suggested by Mark, I am usually deleting all the bonded terms for
the topol.top file and also setting the non-bonded parameter values to
zero in the ffnonbonded.itp file, so that other computations do not
occur and the timing I get only reports that of GB- Energy.
I have done this for different 168 protein molecules and Gromacs is
performing really well and the energy values are comparable with amber
and Octree based approach.
However, for CMV, I am getting an energy value which is almost half of
others. So, to check, now I am not excluding any bonded terms and
using the original force field files provided in gromacs/share/top
folder. Still the value for GB-energy is the same as before :-(.
Here is the log file content (without any modification in .top file
and without the mdrun-rerun command).
Input Parameters:
integrator = md
nsteps = 0
init-step = 0
ns-type = Grid
nstlist = 10
ndelta = 2
nstcomm = 10
comm-mode = Linear
nstlog = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy = 10
nstenergy = 100
nstxtcout = 0
init-t = 0
delta-t = 0.001
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme-order = 4
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = FALSE
ePBC = no
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
bPrintNHChains = FALSE
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
tau-p = 1
ref-p (3x3):
ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
rlist = 1
rlistlong = 1
rtpi = 0.05
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw-switch = 0
rvdw = 1
epsilon-r = 1
epsilon-rf = inf
tabext = 1
implicit-solvent = GBSA
gb-algorithm = HCT
gb-epsilon-solvent = 80
nstgbradii = 1
rgbradii = 1
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = None
sa-surface-tension = 2.25936
DispCorr = No
bSimTemp = FALSE
free-energy = no
nwall = 0
wall-type = 9-3
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = no
rotation = FALSE
disre = No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orires-fc = 0
orires-tau = 0
nstorireout = 100
dihre-fc = 0
em-stepsize = 0.01
em-tol = 10
niter = 20
fc-stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake-tol = 0.0001
lincs-order = 4
lincs-warnangle = 30
lincs-iter = 1
bd-fric = 0
ld-seed = 1993
cos-accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 1.5291e+06
ref-t: 0
tau-t: 0
anneal: No
ann-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm-opts:
ngQM = 0
Initializing Domain Decomposition on 16 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.425 nm, GB 1-4 Pol., atoms 24304 24312
multi-body bonded interactions: 0.425 nm, Proper Dih., atoms 24304 24312
Minimum cell size due to bonded interactions: 0.467 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 16 cells with a minimum initial size of 0.584 nm
The maximum allowed number of cells is: X 43 Y 43 Z 43
Domain decomposition grid 4 x 2 x 2, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0
Detecting CPU-specific acceleration. Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz
Family: 6 Model: 44 Stepping: 2
Features: htt sse2 sse4.1 aes rdtscp
Acceleration most likely to fit this hardware: SSE4.1
Acceleration selected at Gromacs compile time: None
WARNING! Binary not matching hardware - you are likely losing performance.
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: 780.000
Generated table with 1000 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Linking all bonded interactions to atoms
The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell size is: X 6.33 nm Y 12.66 nm Z 12.66 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.000 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.000 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.16 Y 0.00 Z 0.00
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.000 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
Making 3D domain decomposition grid 4 x 2 x 2, home cell index 0 0 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 509700 Atoms
Charge group distribution at step 0: 31431 30755 30753 31435 33210
32021 32023 33214 32024 33215 33217 32028 30752 31434 31432 30756
Grid: 12 x 20 x 20 cells
Initial temperature: 0 K
Started mdrun on node 0 Wed Aug 29 09:58:13 2012
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih.GB Polarization
2.49688e+06 4.48143e+05 1.23111e+06 1.83801e+04 -2.49498e+06
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Potential
8.56489e+05 5.21939e+06 3.98993e+05 -8.11154e+06 6.28585e+04
Kinetic En. Total Energy Temperature Pressure (bar)
7.32160e+06 7.38446e+06 1.15177e+03 0.00000e+00
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 1 steps using 1 frames
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih.GB Polarization
2.49688e+06 4.48143e+05 1.23111e+06 1.83801e+04 -2.49498e+06
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Potential
8.56489e+05 5.21939e+06 3.98993e+05 -8.11154e+06 6.28585e+04
Kinetic En. Total Energy Temperature Pressure (bar)
7.32160e+06 7.38446e+06 1.15177e+03 0.00000e+00
Total Virial (kJ/mol)
-1.57464e+07 5.62500e-01 -2.12500e+00
3.28125e-01 -1.57464e+07 3.25000e+00
-3.67188e+00 -2.68750e+00 -1.57464e+07
Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
Total Dipole (D)
9.76562e-04 0.00000e+00 1.95312e-03
M E G A - F L O P S A C C O U N T I N G
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
Generalized Born Coulomb 1.626204 78.058 0.3
GB Coulomb + LJ 73.629096 4491.375 17.3
Outer nonbonded loop 1.962706 19.627 0.1
1,4 nonbonded interactions 1.348860 121.397 0.5
Born radii (HCT/OBC) 78.053220 14283.739 55.0
Born force chain rule 78.053220 1170.798 4.5
NS-Pairs 245.058526 5146.229 19.8
Reset In Box 0.509700 1.529 0.0
CG-CoM 1.019400 3.058 0.0
Bonds 0.514800 30.373 0.1
Angles 0.934260 156.956 0.6
Propers 1.742760 399.092 1.5
Virial 0.510420 9.188 0.0
Stop-CM 1.019400 10.194 0.0
Calc-Ekin 1.019400 27.524 0.1
-----------------------------------------------------------------------------
Total 25949.137 100.0
-----------------------------------------------------------------------------
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
av. #atoms communicated per step for force: 2 x 103046.0
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Domain decomp. 16 1 2.870 2.0 0.7
Comm. coord. 16 1 0.943 0.6 0.2
Neighbor search 16 1 20.102 13.7 5.0
Force 16 1 132.542 90.4 32.7
Wait + Comm. F 16 1 2.315 1.6 0.6
Update 16 1 0.130 0.1 0.0
Comm. energies 16 1 0.090 0.1 0.0
Rest 16 246.272 167.9 60.8
-----------------------------------------------------------------------
Total 16 405.265 276.3 100.0
-----------------------------------------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 8.635 8.635 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 8.715 3.005 0.010 2398.708
Finished mdrun on node 0 Wed Aug 29 09:58:22 2012
Thanks,
Jesmin
On Wed, Aug 29, 2012 at 1:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 8/29/12 1:06 PM, jesmin jahan wrote:
>>
>> Dear Justin,
>>
>> Thanks for your reply.
>> Here is the CMV.log file . Please check it.
>>
>
> What you've posted is output from grompp. Note that if you're trying to
> send attachments, the list rejects them.
>
>
>>
>> Actually, the .pdb file I am using is already minimized and we are
>> using the same file for amber 11 and Octree based molecular dynamic
>> package.
>
>
> Something doesn't add up. The energy values were indicative of a completely
> unphysical system.
>
>
>> I will also do the minimization step to see what happens.
>>
>> One thing I also want to mention is when I run
>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr command, I get
>> following the log.
>>
>> NOTE 1 [file mdr.mdp]:
>> Tumbling and or flying ice-cubes: We are not removing rotation around
>> center of mass in a non-periodic system. You should probably set
>> comm_mode = ANGULAR.
>>
>
> For a single-point energy evaluation this probably isn't significant.
>
>
>>
>> NOTE 2 [file mdr.mdp]:
>> You are using a cut-off for VdW interactions with NVE, for good energy
>> conservation use vdwtype = Shift (possibly with DispCorr)
>>
>>
>> NOTE 3 [file mdr.mdp]:
>> You are using a cut-off for electrostatics with NVE, for good energy
>> conservation use coulombtype = PME-Switch or Reaction-Field-zero
>>
>>
>
> Finite cutoffs do have a significant outcome of implicit calculations, but
> if you're doing this to remain consistent with other software, I suppose you
> have to keep them as they are.
>
>
>> NOTE 4 [file mdr.mdp]:
>> No SA (non-polar) calculation requested together with GB. Are you sure
>> this is what you want?
>>
>>
>> Generated 2211 of the 2211 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 0.5
>> Generated 2211 of the 2211 1-4 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_A2'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B2'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C2'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A3'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B3'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C3'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A4'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B4'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C4'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A5'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B5'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C5'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A6'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B6'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C6'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A7'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B7'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C7'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A8'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B8'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C8'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A9'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B9'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C9'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A10'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B10'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C10'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A11'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B11'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C11'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A12'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B12'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C12'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A13'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B13'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C13'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A14'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B14'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C14'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A15'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B15'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C15'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A16'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B16'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C16'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A17'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B17'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C17'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A18'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B18'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C18'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A19'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B19'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C19'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A20'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B20'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C20'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A21'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B21'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C21'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A22'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B22'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C22'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A23'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B23'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C23'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A24'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B24'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C24'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A25'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B25'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C25'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A26'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B26'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C26'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A27'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B27'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C27'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A28'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B28'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C28'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A29'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B29'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C29'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A30'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B30'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C30'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A31'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B31'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C31'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A32'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B32'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C32'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A33'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B33'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C33'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A34'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B34'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C34'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A35'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_B35'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C35'
>> ... so on.
>>
>> NOTE 5 [file topol.top, line 388]:
>> System has non-zero total charge: 780.000004
>> Total charge should normally be an integer. See
>> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>> for discussion on how close it should be to an integer.
>>
>>
>>
>> Analysing residue names:
>> There are: 32280 Protein residues
>> Analysing Protein...
>> Number of degrees of freedom in T-Coupling group rest is 1529097.00
>> This run will generate roughly 39 Mb of data
>>
>> There were 5 notes
>>
>> Back Off! I just backed up imd.tpr to ./#imd.tpr.1#
>>
>> gcq#97: "The Universe is Somewhere In Here" (J.G.E.M. Fraaije)
>>
>>
>> I was only interested in non bonded terms (Specially GB-Energy), so I
>> guess, exclusion of bonded terms is not a problem.
>>
>
> How are you excluding bonded terms? If you're hacking the topology to
> remove the bonds, you're going to get a bunch of junk. I haven't followed
> this entire thread fully, but if you're trying to just get certain energies
> and not others, that's what mdrun -rerun is for. You don't initiate an
> mdrun with a broken physical model, otherwise the output will be nonsense.
>
>
> -Justin
>
>> Thanks,
>> Jesmin
>>
>> On Wed, Aug 29, 2012 at 12:09 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>
>>>
>>>
>>> On 8/29/12 11:27 AM, jesmin jahan wrote:
>>>>
>>>>
>>>> Ops!
>>>>
>>>> Thanks Justin for you quick reply.
>>>> Sorry, I have attached a log file from previous run. I am attaching
>>>> the correct log file here. Please have a look.
>>>>
>>>
>>> I don't see a new .log file attached anywhere.
>>>
>>>
>>>> Actually, I am a Computer Science student. I do not have enough
>>>> background of Molecular Dynamics.
>>>> I am using these three commands and
>>>>
>>>> pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none
>>>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr
>>>> OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr
>>>>
>>>> and my .mdp file is like this:
>>>>
>>>> constraints = none
>>>> integrator = md
>>>> pbc = no
>>>> dt = 0.001 ; ps
>>>> nsteps = 0 ; 100000 ps = 100 ns
>>>> rcoulomb = 1
>>>> rvdw = 1
>>>> rlist =1
>>>> nstgbradii = 1
>>>> rgbradii = 1
>>>> implicit_solvent = GBSA
>>>> gb_algorithm = HCT ; OBC ; Still
>>>> sa_algorithm = None
>>>>
>>>>
>>>> What else might go wrong?
>>>>
>>>
>>> The normal workflow included energy minimization before running MD.
>>> Basic
>>> tutorial material covers this. Without EM, you assume that whatever
>>> structure you're using is suitable for MD, which may or may not be true.
>>>
>>> -Justin
>>>
>>>
>>>> Thanks,
>>>> Jesmin
>>>>
>>>> On Wed, Aug 29, 2012 at 11:14 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 8/29/12 11:11 AM, jesmin jahan wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thanks Mark for your reply.
>>>>>>
>>>>>> For the time being, I admit your claim that I am comparing apple with
>>>>>> orange.
>>>>>> So, to investigate more, I run the simulation without any modification
>>>>>> in parameter fields and force field I am using. My test data is CMV
>>>>>> virus shell.
>>>>>> I am using the following commands.
>>>>>>
>>>>>> pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none
>>>>>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr
>>>>>> OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr
>>>>>>
>>>>>>
>>>>>> The log file looks like this:
>>>>>> :-) G R O M A C S (-:
>>>>>>
>>>>>> GROningen MAchine for Chemical Simulation
>>>>>>
>>>>>> :-) VERSION 4.6-dev-20120820-87e5bcf (-:
>>>>>>
>>>>>> Written by Emile Apol, Rossen Apostolov, Herman J.C.
>>>>>> Berendsen,
>>>>>> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton
>>>>>> Feenstra,
>>>>>> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter
>>>>>> Meulenhoff,
>>>>>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland
>>>>>> Schulz,
>>>>>> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>>>>>>
>>>>>> Berk Hess, David van der Spoel, and Erik Lindahl.
>>>>>>
>>>>>> Copyright (c) 1991-2000, University of Groningen, The
>>>>>> Netherlands.
>>>>>> Copyright (c) 2001-2010, The GROMACS development team
>>>>>> at
>>>>>> Uppsala University & The Royal Institute of Technology,
>>>>>> Sweden.
>>>>>> check out http://www.gromacs.org for more information.
>>>>>>
>>>>>> This program is free software; you can redistribute it
>>>>>> and/or
>>>>>> modify it under the terms of the GNU General Public
>>>>>> License
>>>>>> as published by the Free Software Foundation; either
>>>>>> version
>>>>>> 2
>>>>>> of the License, or (at your option) any later version.
>>>>>>
>>>>>> :-) mdrun_mpi (-:
>>>>>>
>>>>>>
>>>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>>>> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
>>>>>> GROMACS 4: Algorithms for highly efficient, load-balanced, and
>>>>>> scalable
>>>>>> molecular simulation
>>>>>> J. Chem. Theory Comput. 4 (2008) pp. 435-447
>>>>>> -------- -------- --- Thank You --- -------- --------
>>>>>>
>>>>>>
>>>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>>>> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H.
>>>>>> J.
>>>>>> C.
>>>>>> Berendsen
>>>>>> GROMACS: Fast, Flexible and Free
>>>>>> J. Comp. Chem. 26 (2005) pp. 1701-1719
>>>>>> -------- -------- --- Thank You --- -------- --------
>>>>>>
>>>>>>
>>>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>>>> E. Lindahl and B. Hess and D. van der Spoel
>>>>>> GROMACS 3.0: A package for molecular simulation and trajectory
>>>>>> analysis
>>>>>> J. Mol. Mod. 7 (2001) pp. 306-317
>>>>>> -------- -------- --- Thank You --- -------- --------
>>>>>>
>>>>>>
>>>>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>>>>> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
>>>>>> GROMACS: A message-passing parallel molecular dynamics implementation
>>>>>> Comp. Phys. Comm. 91 (1995) pp. 43-56
>>>>>> -------- -------- --- Thank You --- -------- --------
>>>>>>
>>>>>> Input Parameters:
>>>>>> integrator = md
>>>>>> nsteps = 0
>>>>>> init-step = 0
>>>>>> ns-type = Grid
>>>>>> nstlist = 10
>>>>>> ndelta = 2
>>>>>> nstcomm = 10
>>>>>> comm-mode = Linear
>>>>>> nstlog = 1000
>>>>>> nstxout = 0
>>>>>> nstvout = 0
>>>>>> nstfout = 0
>>>>>> nstcalcenergy = 10
>>>>>> nstenergy = 100
>>>>>> nstxtcout = 0
>>>>>> init-t = 0
>>>>>> delta-t = 0.001
>>>>>> xtcprec = 1000
>>>>>> nkx = 0
>>>>>> nky = 0
>>>>>> nkz = 0
>>>>>> pme-order = 4
>>>>>> ewald-rtol = 1e-05
>>>>>> ewald-geometry = 0
>>>>>> epsilon-surface = 0
>>>>>> optimize-fft = FALSE
>>>>>> ePBC = no
>>>>>> bPeriodicMols = FALSE
>>>>>> bContinuation = FALSE
>>>>>> bShakeSOR = FALSE
>>>>>> etc = No
>>>>>> bPrintNHChains = FALSE
>>>>>> nsttcouple = -1
>>>>>> epc = No
>>>>>> epctype = Isotropic
>>>>>> nstpcouple = -1
>>>>>> tau-p = 1
>>>>>> ref-p (3x3):
>>>>>> ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> compress (3x3):
>>>>>> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> refcoord-scaling = No
>>>>>> posres-com (3):
>>>>>> posres-com[0]= 0.00000e+00
>>>>>> posres-com[1]= 0.00000e+00
>>>>>> posres-com[2]= 0.00000e+00
>>>>>> posres-comB (3):
>>>>>> posres-comB[0]= 0.00000e+00
>>>>>> posres-comB[1]= 0.00000e+00
>>>>>> posres-comB[2]= 0.00000e+00
>>>>>> rlist = 1
>>>>>> rlistlong = 1
>>>>>> rtpi = 0.05
>>>>>> coulombtype = Cut-off
>>>>>> rcoulomb-switch = 0
>>>>>> rcoulomb = 1
>>>>>> vdwtype = Cut-off
>>>>>> rvdw-switch = 0
>>>>>> rvdw = 1
>>>>>> epsilon-r = 1
>>>>>> epsilon-rf = inf
>>>>>> tabext = 1
>>>>>> implicit-solvent = GBSA
>>>>>> gb-algorithm = HCT
>>>>>> gb-epsilon-solvent = 80
>>>>>> nstgbradii = 1
>>>>>> rgbradii = 1
>>>>>> gb-saltconc = 0
>>>>>> gb-obc-alpha = 1
>>>>>> gb-obc-beta = 0.8
>>>>>> gb-obc-gamma = 4.85
>>>>>> gb-dielectric-offset = 0.009
>>>>>> sa-algorithm = None
>>>>>> sa-surface-tension = 2.25936
>>>>>> DispCorr = No
>>>>>> bSimTemp = FALSE
>>>>>> free-energy = no
>>>>>> nwall = 0
>>>>>> wall-type = 9-3
>>>>>> wall-atomtype[0] = -1
>>>>>> wall-atomtype[1] = -1
>>>>>> wall-density[0] = 0
>>>>>> wall-density[1] = 0
>>>>>> wall-ewald-zfac = 3
>>>>>> pull = no
>>>>>> rotation = FALSE
>>>>>> disre = No
>>>>>> disre-weighting = Conservative
>>>>>> disre-mixed = FALSE
>>>>>> dr-fc = 1000
>>>>>> dr-tau = 0
>>>>>> nstdisreout = 100
>>>>>> orires-fc = 0
>>>>>> orires-tau = 0
>>>>>> nstorireout = 100
>>>>>> dihre-fc = 0
>>>>>> em-stepsize = 0.01
>>>>>> em-tol = 10
>>>>>> niter = 20
>>>>>> fc-stepsize = 0
>>>>>> nstcgsteep = 1000
>>>>>> nbfgscorr = 10
>>>>>> ConstAlg = Lincs
>>>>>> shake-tol = 0.0001
>>>>>> lincs-order = 4
>>>>>> lincs-warnangle = 30
>>>>>> lincs-iter = 1
>>>>>> bd-fric = 0
>>>>>> ld-seed = 1993
>>>>>> cos-accel = 0
>>>>>> deform (3x3):
>>>>>> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>>>>>> adress = FALSE
>>>>>> userint1 = 0
>>>>>> userint2 = 0
>>>>>> userint3 = 0
>>>>>> userint4 = 0
>>>>>> userreal1 = 0
>>>>>> userreal2 = 0
>>>>>> userreal3 = 0
>>>>>> userreal4 = 0
>>>>>> grpopts:
>>>>>> nrdf: 9534
>>>>>> ref-t: 0
>>>>>> tau-t: 0
>>>>>> anneal: No
>>>>>> ann-npoints: 0
>>>>>> acc: 0 0 0
>>>>>> nfreeze: N N N
>>>>>> energygrp-flags[ 0]: 0
>>>>>> efield-x:
>>>>>> n = 0
>>>>>> efield-xt:
>>>>>> n = 0
>>>>>> efield-y:
>>>>>> n = 0
>>>>>> efield-yt:
>>>>>> n = 0
>>>>>> efield-z:
>>>>>> n = 0
>>>>>> efield-zt:
>>>>>> n = 0
>>>>>> bQMMM = FALSE
>>>>>> QMconstraints = 0
>>>>>> QMMMscheme = 0
>>>>>> scalefactor = 1
>>>>>> qm-opts:
>>>>>> ngQM = 0
>>>>>>
>>>>>> Initializing Domain Decomposition on 16 nodes
>>>>>> Dynamic load balancing: auto
>>>>>> Will sort the charge groups at every domain (re)decomposition
>>>>>> Minimum cell size due to bonded interactions: 0.000 nm
>>>>>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>>>>>> Optimizing the DD grid for 16 cells with a minimum initial size of
>>>>>> 0.000
>>>>>> nm
>>>>>> Domain decomposition grid 4 x 4 x 1, separate PME nodes 0
>>>>>> Domain decomposition nodeid 0, coordinates 0 0 0
>>>>>>
>>>>>> Detecting CPU-specific acceleration. Present hardware specification:
>>>>>> Vendor: GenuineIntel
>>>>>> Brand: Intel(R) Xeon(R) CPU X5680 @ 3.33GHz
>>>>>> Family: 6 Model: 44 Stepping: 2
>>>>>> Features: htt sse2 sse4.1 aes rdtscp
>>>>>> Acceleration most likely to fit this hardware: SSE4.1
>>>>>> Acceleration selected at Gromacs compile time: SSE4.1
>>>>>>
>>>>>> Table routines are used for coulomb: FALSE
>>>>>> Table routines are used for vdw: FALSE
>>>>>> Cut-off's: NS: 1 Coulomb: 1 LJ: 1
>>>>>> System total charge: 6.000
>>>>>> Configuring nonbonded kernels...
>>>>>> Configuring standard C nonbonded kernels...
>>>>>>
>>>>>>
>>>>>>
>>>>>> Linking all bonded interactions to atoms
>>>>>>
>>>>>> The initial number of communication pulses is: X 2 Y 2
>>>>>> The initial domain decomposition cell size is: X 0.79 nm Y 0.89 nm
>>>>>>
>>>>>> The maximum allowed distance for charge groups involved in
>>>>>> interactions
>>>>>> is:
>>>>>> non-bonded interactions 1.000 nm
>>>>>> (the following are initial values, they could change due to box
>>>>>> deformation)
>>>>>> two-body bonded interactions (-rdd) 1.000 nm
>>>>>> multi-body bonded interactions (-rdd) 0.794 nm
>>>>>>
>>>>>> When dynamic load balancing gets turned on, these settings will change
>>>>>> to:
>>>>>> The maximum number of communication pulses is: X 2 Y 2
>>>>>> The minimum size for domain decomposition cells is 0.500 nm
>>>>>> The requested allowed shrink of DD cells (option -dds) is: 0.80
>>>>>> The allowed shrink of domain decomposition cells is: X 0.63 Y 0.56
>>>>>> The maximum allowed distance for charge groups involved in
>>>>>> interactions
>>>>>> is:
>>>>>> non-bonded interactions 1.000 nm
>>>>>> two-body bonded interactions (-rdd) 1.000 nm
>>>>>> multi-body bonded interactions (-rdd) 0.500 nm
>>>>>>
>>>>>>
>>>>>> Making 2D domain decomposition grid 4 x 4 x 1, home cell index 0 0 0
>>>>>>
>>>>>> Center of mass motion removal mode is Linear
>>>>>> We have the following groups for center of mass motion removal:
>>>>>> 0: rest
>>>>>> There are: 3179 Atoms
>>>>>> Charge group distribution at step 0: 84 180 252 196 237 210 255 157
>>>>>> 254 197 266 176 186 104 224 201
>>>>>> Grid: 4 x 4 x 4 cells
>>>>>> Initial temperature: 0 K
>>>>>>
>>>>>> Started mdrun on node 0 Wed Aug 29 02:32:21 2012
>>>>>>
>>>>>> Step Time Lambda
>>>>>> 0 0.00000 0.00000
>>>>>>
>>>>>> Energies (kJ/mol)
>>>>>> GB Polarization LJ (SR) Coulomb (SR) Potential
>>>>>> Kinetic
>>>>>> En.
>>>>>> -1.65116e+04 5.74908e+08 -2.37699e+05 5.74654e+08
>>>>>> 6.36009e+11
>>>>>> Total Energy Temperature Pressure (bar)
>>>>>> 6.36584e+11 1.60465e+10 0.00000e+00
>>>>>>
>>>>>> <====== ############### ==>
>>>>>> <==== A V E R A G E S ====>
>>>>>> <== ############### ======>
>>>>>>
>>>>>> Statistics over 1 steps using 1 frames
>>>>>>
>>>>>> Energies (kJ/mol)
>>>>>> GB Polarization LJ (SR) Coulomb (SR) Potential
>>>>>> Kinetic
>>>>>> En.
>>>>>> -1.65116e+04 5.74908e+08 -2.37699e+05 5.74654e+08
>>>>>> 6.36009e+11
>>>>>> Total Energy Temperature Pressure (bar)
>>>>>> 6.36584e+11 1.60465e+10 0.00000e+00
>>>>>>
>>>>>> Total Virial (kJ/mol)
>>>>>> -1.13687e+09 1.14300e+07 -1.23884e+07
>>>>>> 1.14273e+07 -1.15125e+09 -5.31658e+06
>>>>>> -1.23830e+07 -5.31326e+06 -1.16512e+09
>>>>>>
>>>>>> Pressure (bar)
>>>>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>>>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>>>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>>>>>
>>>>>> Total Dipole (D)
>>>>>> 1.35524e+03 -4.39059e+01 2.16985e+03
>>>>>>
>>>>>>
>>>>>> M E G A - F L O P S A C C O U N T I N G
>>>>>>
>>>>>> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
>>>>>> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
>>>>>> NF=No Forces
>>>>>>
>>>>>> Computing: M-Number M-Flops
>>>>>> %
>>>>>> Flops
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----------------------------------------------------------------------------
>>>>>> Generalized Born Coulomb 0.006162 0.296
>>>>>> 0.2
>>>>>> GB Coulomb + LJ 0.446368 27.228
>>>>>> 19.8
>>>>>> Outer nonbonded loop 0.015554 0.156
>>>>>> 0.1
>>>>>> Born radii (HCT/OBC) 0.452530 82.813
>>>>>> 60.3
>>>>>> Born force chain rule 0.452530 6.788
>>>>>> 4.9
>>>>>> NS-Pairs 0.940291 19.746
>>>>>> 14.4
>>>>>> Reset In Box 0.003179 0.010
>>>>>> 0.0
>>>>>> CG-CoM 0.006358 0.019
>>>>>> 0.0
>>>>>> Virial 0.003899 0.070
>>>>>> 0.1
>>>>>> Stop-CM 0.006358 0.064
>>>>>> 0.0
>>>>>> Calc-Ekin 0.006358 0.172
>>>>>> 0.1
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----------------------------------------------------------------------------
>>>>>> Total 137.361
>>>>>> 100.0
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>>>>>>
>>>>>> av. #atoms communicated per step for force: 2 x 7369.0
>>>>>>
>>>>>>
>>>>>> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>>>>>>
>>>>>> Computing: Nodes Number G-Cycles Seconds %
>>>>>>
>>>>>> -----------------------------------------------------------------------
>>>>>> Domain decomp. 16 1 0.210 0.1
>>>>>> 11.4
>>>>>> Comm. coord. 16 1 0.006 0.0
>>>>>> 0.3
>>>>>> Neighbor search 16 1 0.118 0.1
>>>>>> 6.4
>>>>>> Force 16 1 1.319 0.8
>>>>>> 71.4
>>>>>> Wait + Comm. F 16 1 0.016 0.0
>>>>>> 0.9
>>>>>> Update 16 1 0.003 0.0
>>>>>> 0.2
>>>>>> Comm. energies 16 1 0.093 0.1
>>>>>> 5.0
>>>>>> Rest 16 0.082 0.1
>>>>>> 4.4
>>>>>>
>>>>>> -----------------------------------------------------------------------
>>>>>> Total 16 1.847 1.1
>>>>>> 100.0
>>>>>>
>>>>>> -----------------------------------------------------------------------
>>>>>>
>>>>>> NOTE: 5 % of the run time was spent communicating energies,
>>>>>> you might want to use the -gcom option of mdrun
>>>>>>
>>>>>>
>>>>>> Parallel run - timing based on wallclock.
>>>>>>
>>>>>> NODE (s) Real (s) (%)
>>>>>> Time: 0.036 0.036 100.0
>>>>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>>>>>> Performance: 12.702 3.856 2.425 9.896
>>>>>> Finished mdrun on node 0 Wed Aug 29 02:32:21 2012
>>>>>>
>>>>>>
>>>>>>
>>>>>> The GB- energy value reported is half of that reported by Amber 11 and
>>>>>> Octree based Molecular dynamic package.
>>>>>>
>>>>>> Although I guess the difference can be due to the difference in
>>>>>> algorithms they are using, but there could be some other reason.
>>>>>> If anyone knows what are the possible reasons behind this, please let
>>>>>> me know. May be fixing them will give me same value for all different
>>>>>> Molecular Dynamic Package.
>>>>>>
>>>>>
>>>>> I wouldn't trust the result you're getting here - the energy values and
>>>>> temperature (10^10, yikes!) suggest there is something very wrong with
>>>>> the
>>>>> starting configuration.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Research Scientist
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>
>>>>> ========================================
>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users@gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>> interface or send it to gmx-users-requ...@gromacs.org.
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>> ------
>> jesmin
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
--
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