OK, I think I get the right chemical potential. Thank you for answer. Regards,
QHwan -- Kim Q Hwan Center of Nano-Liquid Department of Physics & Astronomy Seoul National University Sent with Sparrow (http://www.sparrowmailapp.com/?sig) On 2014년 10월 9일 Thursday at 오전 2:55, João M. Damas wrote: > Hello Kim, > > 1. Yes, if you choose the cavity location and radius to be inside the water > slab. > > 2. the molecule to be inserted and cavity location are two distinct things. > The molecule to be inserted should be found on the .tpr supplied to mdrun > -rerun. The molecule should be centered at 0, 0, 0 because what the tpic > code does while "inserting" the molecule is to shift the molecule's > position to the inside the cavity you provided by summing a vector > equivalent to the cavity location you supplied (plus a random bit to give a > random location inside the cavity). If the molecule to be inserted is not > centered at 0, 0, 0, it may not be getting inserted where you want it to be > inserted. For Neon, it's trivial to make it centered at 0, 0, 0. ;-) > > 3. the cavity location, unlike the molecule to be inserted, is provided in > the trajectory. There isn't, up to my knowledge, any tool to do this. So > you have to manually edit the original trajectory (keep the original > though). For each frame, you'll have to insert a final line which will have > the coordinates for the cavity location. You probably will have to convert > your trajectory from binary formats to ASCII formats in order to do that > (extra tip: you can construct a script to give different cavity locations > inside the water slab for each frame). > > I hope this helps. > > João > > On Wed, Oct 8, 2014 at 2:49 AM, Kim Q Hwan <[email protected] > (mailto:[email protected])> wrote: > > > Dear all, > > > > I have simulate confined water between two solid crystals with infinite > > XY-periodic dimension. Now I want to calculate the chemical potential of > > the Neon atom in confined water. I think integrator=tpi option is not > > appropriate due to the two solids, so I am using integrator=tpic option. > > > > I have questions. > > > > 1. Is integrator=tpic option appropriate option? > > 2. GROMACS manual says: "The molecule to be inserted should be centered at > > 0,0,0” > > Following this manual, should I center the location of the cavity where > > Neon atom will be inserted to 0, 0, 0? What will happen if the location of > > the cavity is not 0, 0, 0? > > 3. tpic reads the cavity location from the trajectory. But my simulation > > result surely doesn’t contains Neon atom. Is there any script or g_ utility > > including coordinate of the Neon atom to the .trr file? > > > > Thank you. > > -- > > Kim Q Hwan > > Center of Nano-Liquid > > Department of Physics & Astronomy > > Seoul National University > > Sent with Sparrow (http://www.sparrowmailapp.com/?sig) > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected] > > (mailto:[email protected]). > > > > > > > -- > João M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected] (mailto:[email protected]). > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
