Thanks Jason,
Now it is working. One query further in direction..
Can I consider this simulation in continuation of the previous simulation ?
I am asking this question because in this case, the velocity is new and not
related to previous run?
Another silly question is regarding the initial temperature value for this
run.. In my input file, I set the temperature constant at 300K. But the end
of this simulation (at 0 step) the value of temperature was very high..
Although it was normal thereafter.. Is it OK..
NSTEP = 0 TIME(PS) = 1.000 TEMP(K) = 436.65 PRESS =
0.5
Etot = -96680.8541 EKtot = 39933.0595 EPtot =
-136613.9136
BOND = 1149.9344 ANGLE = 2966.4750 DIHED =
3863.4054
1-4 NB = 1302.6612 1-4 EEL = 15965.4034 VDWAALS =
15321.2319
EELEC = -177183.0249 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 11551.1889 VIRIAL = 11545.9990 VOLUME =
443351.4308
Density =
1.0290
------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 3.000 TEMP(K) = 300.01 PRESS =
49.8
Etot = -109366.3000 EKtot = 27437.0234 EPtot =
-136803.3234
BOND = 1124.3275 ANGLE = 2940.1836 DIHED =
3851.2400
1-4 NB = 1302.6532 1-4 EEL = 15987.9748 VDWAALS =
15318.0396
EELEC = -177327.7421 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 11738.3091 VIRIAL = 11261.9237 VOLUME =
443384.1036
Density =
1.0290
------------------------------------------------------------------------------
NSTEP = 2000 TIME(PS) = 5.000 TEMP(K) = 300.89 PRESS =
-14.3
Etot = -108914.6072 EKtot = 27517.3770 EPtot =
-136431.9842
BOND = 1126.7268 ANGLE = 2977.4784 DIHED =
3860.3972
1-4 NB = 1280.0210 1-4 EEL = 15876.2804 VDWAALS =
14875.0134
EELEC = -176427.9013 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 11705.8813 VIRIAL = 11842.8473 VOLUME =
443204.5579
Density =
1.0294
------------------------------------------------------------------------------
roblem. I ran 100ns simulation of my
> > protein-ligand-ion complex in TIP3P. I found that the rmsd value for
> ligand
> > is not stable so thought of continuing the simulation. But I can not use
> > the restart file.
> >
> > I got following error:
> > ERROR: I could not understand line 22288
> > 119.5803932 241.7497484-572.4462595
> >
> >
> > I opened the previous restart file and checked for this line. I found
> that
> > usually there are 6 coordinates in a line (for 2 atoms, if I am not
> wrong).
> > But in the error line there is only 3 coordinate information..
>
> How many atoms do you have in your system? If you have an odd number of
> atoms, then you will have at least 1 line with only 3 numbers.
>
> >
> > 32.4272362 107.0995698 73.2442804 31.4632046 106.0229371 72.7942916
> > 120.3886214 242.0088540-572.8888241 121.0825779 241.7930826-572.2658482
> > 119.5803932 241.7497484-572.4462595
> > -0.0167718 -0.0424197 -0.0394365 0.1475965 0.5324544 0.2035670
> > 0.2566837 -0.1595890 -0.0562660 -0.0466537 0.0079685 -0.1094048
> >
> >
> > I tried to generate the pdb file from last restart file (using ambpdb)
> but
> > it also showed some error.
> >
> > As an alternative, I took previous trajectory file (prod1.crd) and I
> tried
> > to generate the restart file after 50 ns simulation. I managed to
> generate
> > the restart file (also ambpdb worked with with this new restart).
> >
> > BUT, when I restarted my simulation with this restart file, I got
> following
> > error:
> >
> > *ERROR: I could not find enough velocities in restart1.rst*
> >
> >
> > As Dac suggested, I can use the netcdf format in future. But please let
> me
> > know how to restart this simulation 100ns onward???
>
> My guess is that the restart file you printed doesn't have any velocity
> information in it, but you still set irest=1, ntx=5 in your input file.
> This tells sander to use the velocities in the restart file. When they
> can't be found, sander complains. So the solution is to use ntx=1,
> irest=0 to regenerate velocities from a M-B distribution.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Aug 13 2014 - 13:30:02 PDT
