I still want to suggest that segmentation fault doesn't occur due to large no. of insertion molecules the reason being that i, once tried to insert only 1 molecule and it came up with seg. fault again . I am very sure that i have space for atleast some(>1) no. of water molecules. Amit
On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Amit Choubey wrote: > >> Hi everyone, >> >> I have been trying to insert a fixed no. of water molecules in my system. >> I first tried the -cp -cs options and could insert some water molecules. But >> I still need to insert few more water molecules and for that i tried using >> the -nmol -ci option. I made a file named "insert.gro" which has a single >> water molecule with the right volume associated with it. But this option >> gave a segmentation fault and i am not sure why its doing that? May be >> there's not enough space for additional water but it should not give a >> segmentation fault for that reason. Is there something wrong with my idea? >> >> > A segmentation fault with this approach generally indicates that the > requested number of inserted molecules will not fit. > > Alternately, you can try -cs spc216.gro -maxsol (your number) > > If the second approach also fails, I would think that would be strong > evidence that what you're trying to do won't work. > > -Justin > > The insert.gro looks like the following >> >> H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984 >> 3 >> 1SOL OW 1 .130 .128 .113 >> 1SOL HW1 2 .037 .126 .150 >> 1SOL HW2 3 .131 .089 .021 >> 0.31034 0.31034 0.31034 >> >> I also tried various other box (larger) sizes for this but it didnt help. >> Thank you in advance. >> >> Amit >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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