<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div>So, I can not use the coordinates of the output files of gromos runs. Right?<br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Peter C. Lai <pcl@uab.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, April 16, 2012 8:23 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] GROMOS87 and CHARMM27<br> </font> </div> <br>
On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote:<br>> Dear GROMACS users,<br>> <br>> I reproduced the results of a protein-membrane system by using force field GROMOSE87. This protein forms ion channel in membrane.<br>> Now if I wanna study the ion conduction through this channel using force field CHARMM27 in umbrella sampling method, is it possible? Can I use the results of the system simulation which has been derived by GROMOS87?<br><br>By definition, switching to a different forcefield like that usually requires <br>the regeneration of the system's topology, so your new system will be <br>different from your old one anyway. In addition, you may need to rename the <br>atoms in the coordinate files obtained from previous gromos runs to match <br>those in the charmm27 residue files.<br><br>-- <br>==================================================================<br>Peter C. Lai |
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