Thank you all for the reply. Yes I checked my structure there are some
atoms which are very close to each other and thus gives very high energy
when I start my heating step. Minimization does not solve my problem. As
said by Dr. Ross I also verified the initial steps and in the third step
itself the structure is distorted.
When I was using sander earlier, in the first 500 steps of heating the
energy adjusts itself and the structure is relaxed with a sudden drop in
energy . Is it correct. When I use this structure i.e the restrt file in
pmemd.cuda this works fine.
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -6521385.5703 EKtot = 0.0000 EPtot =
-6521385.5703
BOND = 46854.0515 ANGLE = 11499.8085 DIHED =
5254.3722
1-4 NB = -2098.3437 1-4 EEL = 29129.7754 VDWAALS =
-20512.1273
EELEC = -6591513.1069 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.2201E-06
------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 0.500 TEMP(K) = 84.97 PRESS =
0.0
Etot = 58286.0541 EKtot = 5470.0580 EPtot =
52815.9961
BOND = 37269.2949 ANGLE = 11632.2199 DIHED =
4587.7362
1-4 NB = -2070.4722 1-4 EEL = 28519.3325 VDWAALS =
-22369.2241
EELEC = -12345.0692 EHBOND = 0.0000 RESTRAINT =
7592.1781
EAMBER (non-restraint) = 45223.8180
Ewald error estimate: 0.1185E-03
------------------------------------------------------------------------------
Thanks
Kirtana
On Mon, Jun 23, 2014 at 4:11 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Kirtana,
>
> The *'s mean the value is too big to print in the space provided. In this
> case your VDW energy is huge suggesting one of three things:
>
> 1) Your have a bad structure, atoms too close for example - what was the
> final energy from the sander run?
>
> 2) Your restraint energy is also huge - perhaps you are restraining to an
> innapropriate reference structure?
>
> 3) There is a bug in the code.
>
> Firstly I am assuming you are running the minimization with the CPU
> version of the code and then switching to the GPU version for the
> dynamics? - If not then start by doing this. The SPFP precision model is
> very intolerant of strained structures and thus I recommend that one
> always minimizes with the CPU code.
>
> For the dynamics set ntpr=1, nstlim=100, ntwx=1 - then run it and you will
> be able to see what goes wrong at the beginning and visualize it. Note
> tautp in your mdin file has no effect with ntt=3.
>
> Finally check what version of the GPU code you are running (printed early
> on in mdout) - make sure it is fully up to date. It should be 14.0 for
> AMBER 14 and 12.3.1 for AMBER 12.
>
> All the best
> Ross
>
>
> On 6/23/14, 8:40 AM, "kirtana S" <skirtana4.gmail.com> wrote:
>
> >Dear Amber users,
> >
> >If I notice asteriosk or stars marks in my output file and restart file
> > what does this imply. I had this job run in sander without any issues and
> >noticed some error in pmemd cuda. I tried to rectify this by using iwrap 1
> >and still notice similar result.
> >I used mpi run and also single processor run.
> >
> >Can you tell me if the issue is with my input files or my starting
> >structure. Minimization run was preformed on the solvent with restraint on
> >solute before this step.
> >My input file
> >Minimization:
> >&cntrl
> > imin=1, ntx=1,
> > dielc=1.0,ntmin=2,
> > ntrx=1, ntxo=1,
> > ntb=1,ioutfm=1,
> > irest=0, cut=10.0,
> > ntpr=1,
> > maxcyc=10000,
> > ntt=0, ntr=1,
> >&end
> >Hold the PRO fixed
> >40.0
> >RES 1 300
> >END
> >END
> >
> >Second step which give me the error
> >
> >&cntrl
> > imin=0,ntx=1,
> > cut=10.0,tempi=0.0,
> > ntpr=100,ntwx=100,ntwe=100,
> > nstlim=1000000,temp0=100.0,
> > dt=0.001,
> > ntc=2, ntf=2,
> > irest=0,tautp=4.0,
> > ntb=1,iwrap=1,
> > ntt=3,gamma_ln=5.0,ntr=1,
> > &end
> >Hold surface fixed
> >40.0
> >RES 1 300
> >END
> >END
> >
> > NSTEP = 100 TIME(PS) = 0.100 TEMP(K) =********* PRESS =
> >0.0
> > Etot = ************** EKtot = ************** EPtot =
> >**************
> > BOND = -0.0000 ANGLE = 1580104.7120 DIHED =
> >12738.0737
> > 1-4 NB = 0.0000 1-4 EEL = -19.0698 VDWAALS =
> >**************
> > EELEC = -308.1300 EHBOND = 0.0000 RESTRAINT =
> >**************
> > EAMBER (non-restraint) = **************
> >
> >mden file
> >
> >L0 Nsteps time(ps) Etot EKinetic
> >L1 Temp T_solute T_solv Pres_scal_solu
> >L2 Pres_scal_solv BoxX BoxY BoxZ
> >L3 volume pres_X pres_Y pres_Z
> >L4 Pressure EKCoM_x EKCoM_y EKCoM_z
> >L5 EKComTot VIRIAL_x VIRIAL_y VIRIAL_z
> >L6 VIRIAL_tot E_pot E_vdw E_el
> >L7 E_hbon E_bon E_angle E_dih
> >L8 E_14vdw E_14el E_const E_pol
> >L9 AV_permMoment AV_indMoment AV_totMoment Density
> > dV/dlambda
> >L0 100 0.1000000000E+00 0.2542518727E+16 0.2542508165E+16
> >L1 0.3949644593E+14 0.3949644593E+14 0.2525519783E+22 0.1000000000E+01
> >L2 0.1000000000E+01 0.1015340000E+03 0.1656810000E+03 0.3714600000E+02
> >L3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> >L4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> >L5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> >L6 0.0000000000E+00 0.1056199933E+11 0.1970472220E+10 -.3081299803E+03
> >L7 0.0000000000E+00 -.1024454832E-07 0.1580104712E+07 0.1273807373E+05
> >L8 0.0000000000E+00 -.1906978498E+02 0.8589934592E+10 0.0000000000E+00
> >L9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> > 0.0000000000E+00
> >
> >Can you help me with this.
> >
> >Thanks
> >Kirtana
> >_______________________________________________
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>
>
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Received on Mon Jun 23 2014 - 22:00:02 PDT
