AMBER Archive (2005)

Subject: AMBER: Re: Re: AMBER: SHAKE in md with partial solvation

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Mon Jun 06 2005 - 05:49:44 CDT


Hi,Sciaini,

I tried 1 fs time step, but the error remains. I noticed that some hydrogen atoms in fixed residues also moved, so I guess this is not a problem with time step.
 
Best regards,
                                 
Ye Mei
ymei_at_itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2005-06-06

======= 2005-06-06 18:34:09 =======

>
>The time step is high, try with 1ps or 0.5 ps....
>
>Good luck....
>G.
>
>
>At 03:30 p.m. 05/06/2005, you wrote:
>
>>Dear amber usersŁŹ
>>
>>I met a problem with SHAKE in md simulation of a partially solvated
>>system. 20A TIP3P water cap is added to the peptide, around the
>>catalytic site. All residues, including waters, that are more than 15A
>>away from the catalytic site are not allowed to move. The system is first
>>minimized in 2000 steps, followed by 2000 steps heat-up with step size
>>2fs. Then the constant temperature md simulation is performed. SHAKE is
>>implemented in both heat-up and constant temperature md simulation. But an
>>error message says:
>>
>> NSTEP = 4500 TIME(PS) = 13.000 TEMP(K) = 306.89 PRESS
>> = 0.0
>> Etot = -2812.1921 EKtot = 1628.5984 EPtot =
>> -4440.7905
>> BOND = 362.2453 ANGLE = 1021.4029 DIHED =
>> 1348.8158
>> 1-4 NB = 441.4590 1-4 EEL
>> = 5960.7192 VDWAALS = -434.6513
>> EELEC = -13140.7814 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>>
>>------------------------------------------------------------------------------
>>
>> vlimit exceeded for step 4580 ; vmax = 44.619679589066607
>>
>> Coordinate resetting (SHAKE) cannot be accomplished,
>> deviation is too large
>> NITER, NIT, LL, I and J are : 0 2 638 1406 1405
>>
>> Note: This is usually a symptom of some deeper
>> problem with the energetics of the system.
>>
>>Then I checked the heated structure, and found that those residues which
>>should be kept fixed in heat-up procedure also have their coordinates
>>changed. The constant temperature md simulation died because some
>>hydrogens moved far away from atoms they connect to.
>>Is there anything wrong with my input files in the attachment? Or how to
>>keep those faraway residues fixed during md simulation?
>>ĄĄĄĄĄĄĄĄĄĄĄĄ
>>
>>Best regards,
>>
>>Ye Mei
>>ymei_at_itcc.nju.edu.cn
>>Institute of Theoretical and Computational Chemistry
>>Key Laboratory of Mesoscopic Chemistry
>>School of Chemistry and Chemical Engineering
>>Nanjing University
>>Nanjing 210093
>>P.R.China
>>2005-06-05
>>
>>
>>
>>
>>
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>
>
>
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>
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