[gmx-users] Invitation to connect on LinkedIn
LinkedIn Zhao Lifeng requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Zhao Accept invitation from Zhao Lifeng http://www.linkedin.com/e/-85v1n9-gpeoratj-d/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I2918122309_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnPAMcP8OcjwNej99bSxOi4VSi7FFbPsSejwSczgQcPcLrCBxbOYWrSlI/EML_comm_afe/ View invitation from Zhao Lifeng http://www.linkedin.com/e/-85v1n9-gpeoratj-d/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I2918122309_2/39vej0Pcz8Ne34VcAALqnpPbOYWrSlI/svi/ -- (c) 2011, LinkedIn Corporation-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Re: Alchemistry free energy simulations of molecules with different atom numbers
> > On Wed, Nov 19, 2008 at 2:14 PM, Zhao Lifeng <[EMAIL PROTECTED]> wrote: > > > > > Dear all, > > > > I encountered a problem in alchemistry free energy calculations: > > > > In my simulations a group (A) is to be changed to (B) in a molecule, > while > > the atom numbers n(A) is not equal to n(B). > > A scheme is to include both A and B in the same topology file and switch > > on/off the B/A charges and vdw interactions. > > And interactions between A and B were excluded in the simulations. > However, > > the vibration mode would not be correct > > for both A and B state. > > > > Another scheme is to change the corresponding atoms to zero mass dummy > > atoms or from them. In this case, there will be > > no interactions on the dummy atoms, either bonded or non-bonded > > interactions. > > > > I don't know if these schemes are correct and if there is any other more > > reasonable schemes. In my simulations I prefered the > > later one and thus the problems came. > > In state of lambda=0 or =1, since there are dummy atoms with no force on > > them, (sometimes with velocities, e.g. from > > the last lambda simulation), the dummy atoms often bring forth errors, > > for example, 1-4 distance too large, neighbor list error > > and segmentation fault. Bond constraints seems work but it might not be > > reasonable for heavy atoms. > > > > Any suggestions would be appreciated. > > > Hello, > > I have used schemes similar to the one you described and to circumvent the > problems associated with growing or disappearing particles out of nothing > I > used soft-core interactions and manipulated the soft-core parameters to get > "nice" dgdl curves. Hope this helps. > > Diana Lousa > PhD student > Protein Modelling Laboratory > ITQB/UNL > Oeiras, Portugal > > > > > Lifeng Zhao > Thanks Diana. But softcore does not help for it only affect vdw interactions. In my TI simulation case, the dummy atoms has no mass and the bond interactions are turned off. (If bond interactions were not turned off there would produce a segmentation fault for forces on zero mass.) Lifeng Zhao ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Alchemistry free energy simulations of molecules with different atom numbers
Dear all, I encountered a problem in alchemistry free energy calculations: In my simulations a group (A) is to be changed to (B) in a molecule, while the atom numbers n(A) is not equal to n(B). A scheme is to include both A and B in the same topology file and switch on/off the B/A charges and vdw interactions. And interactions between A and B were excluded in the simulations. However, the vibration mode would not be correct for both A and B state. Another scheme is to change the corresponding atoms to zero mass dummy atoms or from them. In this case, there will be no interactions on the dummy atoms, either bonded or non-bonded interactions. I don't know if these schemes are correct and if there is any other more reasonable schemes. In my simulations I prefered the later one and thus the problems came. In state of lambda=0 or =1, since there are dummy atoms with no force on them, (sometimes with velocities, e.g. from the last lambda simulation), the dummy atoms often bring forth errors, for example, 1-4 distance too large, neighbor list error and segmentation fault. Bond constraints seems work but it might not be reasonable for heavy atoms. Any suggestions would be appreciated. Lifeng Zhao ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About calculations of viscosity
Dear gmx-users, I’m a new GMX user. I notice from either the user-manual or the references (Palmer, PRE 49 359, & B. Hess, JCP 116, 209, etc.) that there seem to be at least 3 methods available in Gromacs: Einstein relation, TCAF and periodic perturbation method. But I’m not very clear about how to set the calculations and how to get the according viscosity values. My understanding is this: For Einstein relation calculations, there is no special setting in the md.mdp file, and the viscosity value is gotten by the visco.xvg file generated by ‘g_energy �Cvis’; For TCAF, also there is no special setting in the md.mdp file, and the viscosity value is gotten by fitting the data of visco_k.xvg file generated by ‘g_tcaf’; For the periodic perturbation method, two NEMD items, a ‘accelerate’ value in X direction should be specified to all atoms and a ‘cos_acceleration’ value should be given, and the viscosity value is gotten from the ‘1/Viscosity(SI)’ item of the ‘g_energy’ results. I’m eager for any instructions about techniques on the calculations and the value ranges. Thanks. Zhao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
