Minimize the system before doing any MD. The default maximum velocity
limit is 20 in amber's internal units (angstroms/picosecond(?)). This
is usually sufficiently in excess of the fastest velocity that appears
in *equilibrated* simulations. The fact that you're getting
velocities magnitudes of order greater than the limit suggests that
you have overlapping atoms, and the van der waals clash is supplying a
repulsive force significantly large to induce such large velocities.
A short minimization should relax these bad contacts, and careful
heating (as described above) should help you achieve proper behavior.
Good luck!
Jason
2010/1/2 John S <s.john634.gmail.com>:
> Even after heating the temperature gradually as suggested , it gives the
> same error message in my md.out file .
>
> Thanks for your suggestion .
>
> John
>
> On Sat, Jan 2, 2010 at 10:32 AM, xmzpzengs <xmzpzengs.gmail.com> wrote:
>
>> you must heat your system slowly.
>> set tempi=0 temp0=300
>> try again.
>>
>> ------------------
>> Name：Zeng Zhi-Ping Ph.D
>> Email：zengzhiping.xmu.edu.cn
>> interest: organic phosphorus chemistry and drug design
>> software：DOCK6.2;AUTODOCK4.0;AMBER10;
>> address：Department of Chemistry, Xiamen University,
>> the Key Laboratory for Chemical Biology of Fujian Province,
>> Xiamen 361005, People's Republic of China
>> 2010-01-02
>>
>> -------------------------------------------------------------
>> 发件人：John S
>> 发送日期：2010-01-02 23:15:55
>> 收件人：AMBER
>> 抄送：
>> 主题：[AMBER] vlimit exceeded
>>
>> Dear Amber users,
>>
>> While running NVT molecular dynamics production run I get the following
>> error messages in my md.out file :
>>
>> vlimit exceeded for step 14024; vmax = 1999.5604
>> vlimit exceeded for step 14025; vmax = 47616.4710
>> vlimit exceeded for step 14026; vmax = 4368.5140
>> vlimit exceeded for step 14027; vmax = 9412.1124
>> vlimit exceeded for step 14028; vmax = 7444.361
>>
>> My md.in file :
>>
>> md
>> &cntrl
>> imin=0, ntx=1,
>> irest=0, ntxo=1,cut=15.0, tempi=300.0,
>> ntpr=1000, ntwx=1000, ntwe=1000,
>> nstlim=10000000,tautp=2, temp0=300.0,
>> dt=0.001, nscm=100,
>> igb=0, ntb=1,ntp=0, ntt=1, nsnb=20,
>>
>> Thanks for your help and suggestion .
>>
>> John.
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>>
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>>
>>
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jan 02 2010 - 10:30:03 PST
