Hi Aparna
Your restraint energy is pretty high. I suspect this is what might be
causing the problem. What are you using as your reference structure for the
restraints? And what is the restraint force constant set to?
Also try NTT=1 instead of NTT=3 if that is what you are using. NTT=3 tends
to have problems with restraints sometimes in my experience.
All the best
Ross
> -----Original Message-----
> From: Aparna P [mailto:aparnaspap.gmail.com]
> Sent: Monday, September 12, 2011 10:04 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] vlimit exeeding problem
>
> Thanks a lot for your reply sir.
> I tried with 1fs.Now there is difference in the output.
> But still the same problem is there after 62ps.
>
> =======================================================================
> ========
>
> NSTEP = 12500 TIME(PS) = 62.500 TEMP(K) = 215.10 PRESS =
> 0.0
> Etot = -43622.7596 EKtot = 5467.7295 EPtot =
> -49090.4891
> BOND = 143.5801 ANGLE = 701.6306 DIHED =
> 591.4445
> 1-4 NB = 268.4208 1-4 EEL = -5545.9446 VDWAALS =
> 7033.4256
> EELEC = -52388.2026 EHBOND = 0.0000 RESTRAINT =
> 105.1565
> EAMBER (non-restraint) = -49195.6456
> Ewald error estimate: 0.3473E-04
> ----------------------------------------------------------------------
> --------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
> 0.000
> =======================================================================
> ========
> vlimit exceeded for step 12659; vmax = 22.8267
> vlimit exceeded for step 12660; vmax = 21.3374
> vlimit exceeded for step 12661; vmax = 22.2267
> vlimit exceeded for step 12666; vmax = 22.5449
> vlimit exceeded for step 12708; vmax = 20.6433
> vlimit exceeded for step 12711; vmax = 21.4597
> vlimit exceeded for step 12755; vmax = 20.9151
> vlimit exceeded for step 12757; vmax = 23.1312
> vlimit exceeded for step 12760; vmax = 20.0437
> vlimit exceeded for step 12764; vmax = 20.3647
> vlimit exceeded for step 12767; vmax = 21.1798
>
> but after 62ps it didn't show any problem.
> I have visualised the trajectories in vmd and it showed some
> distortions.
> I don't know what happened to the structure.
> The minimisation is done successfully.
>
> Kindly give a suggestion.
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Received on Mon Sep 12 2011 - 22:30:04 PDT
