[AMBER] how to simulate solute in vacuum with TI

From: Junjian Miao <junjianmiao.gmail.com>
Date: Wed, 23 Feb 2011 09:34:19 +0800

Hi all,

 

thank you very much for your last reply. now i meet some trouble again in the course of learning TI. the following is a process of transformation in vacuo.

 



 

with respect to step1, are the simulation conditions such as ¡°cut, gamma_ln, ntf, ntc, temp0¡± must identical to aqueous phase? can i modify the ¡°cut¡± larger for step1?

 

 

with respect to step2, you say there is no need to simulate, DVdl is always equal to 0. however, if i simulate this step, how to create the input files. i have a try, but get the following errors

     
     [jjmiao.cu15 BAR1]$ forrtl: severe (174): SIGSEGV, segmentation fault occurred

            Image PC Routine Line Source

            sander.MPI 00000000005BD01D Unknown Unknown Unknown

            sander.MPI 00000000005BA1AA Unknown Unknown Unknown

            sander.MPI 00000000005C040E Unknown Unknown Unknown

            sander.MPI 00000000004F1A7A Unknown Unknown Unknown

            sander.MPI 00000000004B9549 Unknown Unknown Unknown

            sander.MPI 00000000004B8262 Unknown Unknown Unknown

            sander.MPI 0000000000405982 Unknown Unknown Unknown

            libc.so.6 0000003C52A1D8A4 Unknown Unknown Unknown

            sander.MPI 00000000004058A9 Unknown Unknown Unknown

            forrtl: No such file or directory

            forrtl: No such file or directory

                                              ¡­¡­
           
        
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 



with sander.MPI, can i simulate step2 successfully? although it is not necessary.

 

thank you in advance

Junjian

 





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Received on Tue Feb 22 2011 - 18:00:07 PST
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