Hi Ross.
I've modified the parameters in the input files and run a short
simulation. I've also removed the nmropt parameter, used a smaller dt =
0.001 for heating and the default cut off value as Dave Case suggested.
> heat 1modnew pdb model
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=200,dt=0.001,
> ntc=2,ntf=2,
> cut=8.0, ntb=1,
> ntpr=1, ntwx=1,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=300.0,
> ntr=1, restraintmask=':1-359',
> restraint_wt=2.0,
> /
> &wt TYPE='TEMP0', istep1=0, istep2=200,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
For the first 100 steps, everything runs smoothly, however when it
reaches 121st step, something happens and the systems stops recording
the coordinates.
> NSTEP = 117 TIME(PS) = 0.117 TEMP(K) = 210.25 PRESS
> = 0.0
> Etot = -112811.5087 EKtot = 18668.2268 EPtot =
> -131479.7355
> BOND = 390.1195 ANGLE = 1336.7571 DIHED =
> 3603.8211
> 1-4 NB = 1248.9758 1-4 EEL = 15140.5116 VDWAALS =
> 14765.1944
> EELEC = -168653.7188 EHBOND = 0.0000 RESTRAINT =
> 688.6038
> EAMBER (non-restraint) = -132168.3393
> Ewald error estimate: 0.1734E-03
> ------------------------------------------------------------------------------
>
>
> NSTEP = 118 TIME(PS) = 0.118 TEMP(K) = 210.78 PRESS
> = 0.0
> Etot = -112763.9758 EKtot = 18714.8203 EPtot =
> -131478.7961
> BOND = 390.5795 ANGLE = 1343.1895 DIHED =
> 3603.8457
> 1-4 NB = 1250.2384 1-4 EEL = 15140.6781 VDWAALS =
> 14771.7984
> EELEC = -168670.8462 EHBOND = 0.0000 RESTRAINT =
> 691.7206
> EAMBER (non-restraint) = -132170.5167
> Ewald error estimate: 0.1705E-03
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 118; vmax = 21.8903
>
> NSTEP = 119 TIME(PS) = 0.119 TEMP(K) = 211.22 PRESS
> = 0.0
> Etot = -112727.1844 EKtot = 18753.6200 EPtot =
> -131480.8044
> BOND = 388.9545 ANGLE = 1345.8846 DIHED =
> 3603.9459
> 1-4 NB = 1251.5202 1-4 EEL = 15140.8237 VDWAALS =
> 14778.4999
> EELEC = -168685.3843 EHBOND = 0.0000 RESTRAINT =
> 694.9510
> EAMBER (non-restraint) = -132175.7554
> Ewald error estimate: 0.1604E-03
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 119; vmax = 33.8437
>
> NSTEP = 120 TIME(PS) = 0.120 TEMP(K) = 211.56 PRESS
> = 0.0
> Etot = -112697.9928 EKtot = 18784.1577 EPtot =
> -131482.1505
> BOND = 385.8065 ANGLE = 1345.0881 DIHED =
> 3604.0054
> 1-4 NB = 1252.6871 1-4 EEL = 15140.7684 VDWAALS =
> 14786.4738
> EELEC = -168695.3038 EHBOND = 0.0000 RESTRAINT =
> 698.3240
> EAMBER (non-restraint) = -132180.4745
> Ewald error estimate: 0.1500E-03
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 120; vmax = 20.7846
>
> NSTEP = 121 TIME(PS) = 0.121 TEMP(K) = NaN PRESS
> = 0.0
> Etot = NaN EKtot = NaN EPtot =
> -131478.1093
> BOND = 382.1245 ANGLE = 1341.7938 DIHED =
> 3604.0781
> 1-4 NB = 1253.8178 1-4 EEL = 15140.7402 VDWAALS =
> 14798.0296
> EELEC = -168700.5153 EHBOND = 0.0000 RESTRAINT =
> 701.8221
> EAMBER (non-restraint) = -132179.9314
> Ewald error estimate: 0.1487E-03
> ------------------------------------------------------------------------------
>
>
> NSTEP = 122 TIME(PS) = 0.122 TEMP(K) = NaN PRESS
> = 0.0
> Etot = NaN EKtot = NaN EPtot
> = NaN
> BOND = 378.6183 ANGLE = 1337.7266 DIHED =
> 3604.4706
> 1-4 NB = 1255.0961 1-4 EEL = 15140.7367 VDWAALS
> = NaN
> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
> 705.3260
> EAMBER (non-restraint) = NaN
> Ewald error estimate: 0.0000E+00
> ------------------------------------------------------------------------------
>
>
> NSTEP = 123 TIME(PS) = 0.123 TEMP(K) = NaN PRESS
> = 0.0
> Etot = NaN EKtot = NaN EPtot
> = NaN
> BOND = NaN ANGLE = 712532.6268 DIHED
> = 0.0000
> 1-4 NB = NaN 1-4 EEL = NaN VDWAALS =
> -1264.8700
> EELEC = NaN EHBOND = 0.0000 RESTRAINT
> = NaN
> Ewald error estimate: 0.0000E+00
> ------------------------------------------------------------------------------
>
>
> NSTEP = 124 TIME(PS) = 0.124 TEMP(K) = NaN PRESS
> = 0.0
> Etot = NaN EKtot = NaN EPtot
> = NaN
> BOND = NaN ANGLE = 712532.6268 DIHED
> = 0.0000
> 1-4 NB = NaN 1-4 EEL = NaN VDWAALS =
> -1264.8700
> EELEC = NaN EHBOND = 0.0000 RESTRAINT
> = NaN
> Ewald error estimate: 0.0000E+00
> ------------------------------------------------------------------------------
>
>
> NSTEP = 125 TIME(PS) = 0.125 TEMP(K) = NaN PRESS
> = 0.0
> Etot = NaN EKtot = NaN EPtot
> = NaN
> BOND = NaN ANGLE = 712532.6268 DIHED
> = 0.0000
> 1-4 NB = NaN 1-4 EEL = NaN VDWAALS =
> -1264.8700
> EELEC = NaN EHBOND = 0.0000 RESTRAINT
> = NaN
> Ewald error estimate: 0.0000E+00
> ------------------------------------------------------------------------------
I've checked the md coordinate files and it recorded coordinates up to
120 and after that nothing, everything becomes NaN.
I looked carefully at the coordinates of the mutant, they seem fine the
change is minor. I am really out of ideas as what is happening.
Can you please suggest where else can I look to solve the problem?
Thank you,
Cristina
Ross Walker wrote:
> Hi Cristina,
>
>
>>> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
>>> = 0.0
>>> Etot = -119235.7327 EKtot = 0.0000 EPtot =
>>> -119235.7327
>>> BOND = 120.1323 ANGLE = 762.7237 DIHED =
>>> 3442.2867
>>> 1-4 NB = 1372.0187 1-4 EEL = 15491.2504 VDWAALS =
>>> 4621.6183
>>> EELEC = -145045.7628 EHBOND = 0.0000 RESTRAINT
>>> = 0.0000
>>> Ewald error estimate: 0.4162E-03
>>> --------------------------------------------------------------------
>>>
>> ----------
>>
>>> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>>>
>> 0.000
>>
>> =======================================================================
>> ========
>>
>>> vlimit exceeded for step 2; vmax = 33.0050
>>> vlimit exceeded for step 3; vmax = 25.9657
>>>
>
> The energies look fine and very similar to other mutant which doesn't show
> this. You may find that this is transient and you can ignore it, if it only
> happens on the first few steps you might be okay. The best option though
> would be to try running a short 100 step or so run and recording the
> coordinates every step. Then you can look and see if anything looks strange.
> It is also possible to put a print statement in the vlimit code to show
> which atom is exceeding the limit.
>
> Try
>
> nstlim=100, ntwx=1, ntpr=1,
>
> And watch it in VMD and see if you can see what is happening. Note the
> vlimit default is 20 so the above numbers are fairly close to the limit
> where they wouldn't show up.
>
>
>> I do not see any major differences however, one is running and one is
>> not.
>>
>
> When you say one is not, does it crash with an error? Or just give you
> vlimits for the first few steps and then continue?
>
>
>> The input file that I use is:
>>
>>> heat 1modnew pdb model
>>> &cntrl
>>> imin=0,irest=0,ntx=1,
>>> nstlim=25000,dt=0.002,
>>> ntc=2,ntf=2,
>>> cut=11.0, ntb=1,
>>> ntpr=500, ntwx=500,
>>> ntt=3, gamma_ln=2.0,
>>> tempi=0.0, temp0=300.0,
>>> ntr=1,
>>> restraint_wt=2.0,
>>> nmropt=1,
>>> restraintmask = '(:1-359)',
>>> /
>>> &wt TYPE='TEMP0', istep1=0, istep2=25000,
>>> value1=0.1, value2=300.0, /
>>> &wt TYPE='END' /
>>>
>
> There may be something going wrong in the restraints. Note you probably
> don't need the brackets in the expression above. Check that the number of
> atoms you expect is being found. Running with NTPR=1 will also help you see
> if the restraint energy suddenly shoots up.
>
>
>> I checked the system after the minimization step and it looked fine. I
>>
>
> How long did you minimize for? Also did you have shake on when you did the
> minimization? If you didn't then you will have H atoms at 'non-shake'
> distances and then you are using this as a reference for your restraints
> which means you will always get restraint forces due to shake trying to
> reset the H atom positions. Just a guess but it is possible this is causing
> issues. You could also try minimizing some more, what was the RMS and GMAX
> forces at the end of the minimization? - Which atom did it list as having
> the most force on it? - This is likely to be where any problems lie.
>
> Good luck,
>
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
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Received on Tue Jun 22 2010 - 06:30:03 PDT
