"
But the *end *of this simulation (at 0 step) the value of
temperature......."
Ohh.. Its sleeping time now. I meant "But *at the beginning* of simulation
(at step 0)......"
On Wed, Aug 13, 2014 at 10:15 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
wrote:
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Aug 13 2014 - 13:30:02 PDT
