Re: [gmx-users] Where to locate the functional form of [ bonds ], [ angles ] and [ dihedrals ]?

Thanks Mark.! That helps a lot.! =D =D =D Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry Biological Chemistry School of Physical Mathematical Sciences | Nanyang Technological University | Singapore 639798 Tel: (+65) 97967803 | Email: yipy0...@e.ntu.edu.sg | GMT+8h

[gmx-users] Obtaining Positive Energy Values for Both Potential and Total Energies

. I checked the density and it seems fine. There are no warning or abrupt ceasing of the equilibration run due to system blow-up. Therefore, I wish to ask if it’s normal to observe such trends for those energy values? Thanks. Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry

[gmx-users] Where to locate the functional form of [ bonds ], [ angles ] and [ dihedrals ]?

Hi, I know certain functional forms are represented by certain integers in the .itp files. As I’m constructing my own .itp file, I wish to know where is a possible place for me to find out which integer represents which functional form? Thanks, any help is greatly appreciated. =) Yip Yew Mun

[gmx-users] How To Turn Off Electrostatics Linearly in TI Simulations

to 0 angstroms? If not, what is the technical action to execute in the mdp file? Thanks. On 7/13/14, 10:10 AM, Yip Yew Mun wrote: Hi all, I?m planning to run thermodynamic integration (TI) simulations with a few lambda values. I read articles and found out that the one of the better ways

[gmx-users] Requesting for Help on Hybrid CG-AA MD Simulations

Hi all, I wish to run a MD simulation with the protein in CG and the small organic ligand in AA. Has anyone attempted this before? If so, can guide me on how to generate the right topologies for such simulations? Thanks, any help would be greatly appreciated. =) Yip Yew Mun (Mr) | PhD

[gmx-users] Requesting help on converting a CG (coarse grained) trajectory to a FG (fine grained) trajectory

this action. Thanks, any help is greatly appreciated. =) Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry Biological Chemistry School of Physical Mathematical Sciences | Nanyang Technological University | Singapore 639798 Tel: (+65) 97967803 | Email: yipy0...@e.ntu.edu.sg | GMT

[gmx-users] Some basic questions about trajconv

would be greatly appreciated. =) Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry Biological Chemistry School of Physical Mathematical Sciences | Nanyang Technological University | Singapore 639798 Tel: (+65) 97967803 | Email: yipy0...@e.ntu.edu.sg | GMT+8h -- Gromacs Users