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<DIV class=RTE>Dear all</DIV>
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<DIV class=RTE>When i use gromacs in dynamics simulation,i get trouble with the huge .trr file which is 5G and unable to open.I have seen your mail in gromacs mail lists on how to solve this problem about huge .trr file.i have not understand it completly because i am a new user.so,there are three questions as follows i want to consult you:</DIV>
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<DIV class=RTE><STRONG>1/</STRONG> when runing mdrun,how can i keep water molecule out of the output file(such as.trr) in order to minmize the size of the outpur file</DIV>
<DIV class=RTE><STRONG>2/</STRONG> according to what you said in gromacs mail lists: "<STRONG>if you use the .xtc file format then you don't have to save to ..trr very often at all, only really the final step if you want to extend the simulation. This can be wasteful though, as if your simulation crashes somewhere then you have to start from the very start again and there can go a significant amount of CPU time. Personally I have mine save every about 6 hours real time and only keep the last .trr file so if the need arises I can continue the simulation. Everything else is saved and archived as .xtc"</STRONG></DIV>
<DIV>i do not understand what you said above.if you only use the .xtc file as output file,how did you save the position and velocities to .trr file? if you use both .trr and .xtc file as out files,how did you divide the .trr file every 6 hours when mdrun was running? terminated the mdrun ,delete the .trr file every 6 hours or other method? This point confuse me most,please give me a detailed interpretation. thank you!!! </DIV>
<DIV><STRONG>3/ </STRONG>How to use trjconv remove all the atoms that are not of importance to see fromthetrajectory, such as water/SOL.i want to know which option trjconv command used can function.please give me a command line.</DIV>
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<DIV>Thanks in advance</DIV>
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<DIV>XuDong Zhang<BR>center of Biology <BR>YunNan University<BR><A href="mailto:zhangxd@ynu.edu.cn">zhangxd@ynu.edu.cn</A></DIV>
<DIV><A href="mailto:zxdcs@hotmail.com">zxdcs@hotmail.com</A><BR>(86) 871 5035727<BR><BR><BR> </DIV>
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