Re: [AMBER] The problem of restart file

From: Jeffrey <jeffry20072008.yahoo.cn>
Date: Wed, 1 Jul 2009 15:07:08 +0100

Thanks so much for your prompt response.
 I checked the final .rst file and didn't find a * character. But the coordinates corresponding to the solvent waters have very large absolute values, which suggests that the some water molecules run far away from the primary unit (see below). I don't know whether amber can read the coordinates from .rst file if two coordinates are placed without no space between them, such as 262.8406697-285.5083095 ?

When the wrapping option is turned on at the final .rst file, are the trajectories produced with iwrap=1 consistent with the previous ones with iwrap=0?

part of .rst file:
-------
 838.3034031 222.7643257 376.2435746 838.3937838 223.6324042 376.6366432
 838.1837141 222.9356520 375.3094687 54.2277689-330.7610570 42.3999106
  53.6300875-331.0916131 43.0705383 54.9146661-331.4252468 42.3428492
 262.8406697-285.5083095 41.7790696 262.7365183-284.6234116 42.1288410
 262.7950086-286.0766640 42.5479129-112.4590544 -18.4847370 145.5590728
-112.6763470 -19.2162691 146.1368933-112.6717653 -17.7041295 146.0705782
 -94.4094824-131.8181207 -28.8877479 -93.8192046-131.6759820 -28.1477475
----------------


Many thanks.


Jeffrey.




--- 09年7月1日,周三, Carlos Simmerling <carlos.simmerling.gmail.com> 写道:


发件人: Carlos Simmerling <carlos.simmerling.gmail.com>
主题: Re: [AMBER] The problem of restart file
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2009年7月1日,周三,下午8:49


it looks like it might be that the coordinates are too large to fit the
restart format. you can confirm by visually inspecting the restart file and
looking for * characters.
it usally happens in a long run because the water diffuses so far from the
origin. this can be avoided in long runs by turning on wrapping (iwrap=1)


2009/7/1 Jeffrey <jeffry20072008.yahoo.cn>

> Dear AMBER users,
>
> I performed a long md simulation by repeating restarts. But at the 28th
> segment, the simulation can't be continued because the pmemd can't open the
> restart file (npt28.rst). Here are some error message:
> in .out file:
> ---
> ....
> &cntrl
> imin=0,
> ntx=5, irest=1,
> ntpr=100, ntwx=1000,ntwr=5000,
> dt=0.002,nstlim=1000000, nscm=1000,
> cut=9.,dielc=1.0,
> ntc=2, ntf=2,
> ntb=2,
> ntp=1,pres0=1.0,taup=3.0,
> ntt=1, tautp=3.0,temp0=300.0,
> ioutfm=1
> /
> | ERROR: Could not read coords from npt28.rst
> ---------------
>
> When using ambpdb to convert from npt28.rst to npt28.pdb using the command:
> ambpdb -p mono10.prmtop < npt28.rst > npt28.pdb
>
> errors are:
> ------------
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/19/09 Time = 22:55:51
> forrtl: severe (64): input conversion error, unit 5, file stdin
> Image PC Routine Line Source
> ambpdb 00000000004A593E Unknown Unknown Unknown
> ambpdb 00000000004A4B3E Unknown Unknown Unknown
> ambpdb 000000000045498A Unknown Unknown Unknown
> ambpdb 000000000041E172 Unknown Unknown Unknown
> ambpdb 000000000041D9A1 Unknown Unknown Unknown
> ambpdb 0000000000439716 Unknown Unknown Unknown
> ambpdb 000000000040D194 Unknown Unknown Unknown
> ambpdb 00000000004058FD Unknown Unknown Unknown
> ambpdb 00000000004034CC Unknown Unknown Unknown
> libc.so.6 0000003083C1D8A4 Unknown Unknown Unknown
> ambpdb 00000000004033D9 Unknown Unknown Unknown
> -----------
>
>
> Does anyone encounter the similar problems?
> Any suggestion is greatly appreciated.
>
> Thanks.
>
>
> Jeffry
>
>
> -----------
> Dalian Institute of Chemical Physics,
> Chinese Academy of Sciences
> Dalian, China
> _______________________________________________
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>
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Jeffrey Yang

-----------
Dalian Institute of Chemical Physics,
Chinese Academy of Sciences
Dalian, China


Received on Mon Jul 06 2009 - 12:27:58 PDT
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