[gmx-users] bug for TIP4P water in GROMACS ?

2012-02-13 Thread GZ Zhang
Hi, ALL Has anyone heard that there has been a bug in the energy calculation of TIP4P water in older GROMACS (from v3.3 to v4.0.5) ? Thanks ! Guozhen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] how does gromacs handle the force on the virtual site of the TIP4P model

2012-02-09 Thread GZ Zhang
Hi, ALL We are writing our own MD program to simulate water and the TIP4P model is being considered. I am wondering that how does GROMACS program handle the force on the massless M site of the TIP4P model? It would be better to be informed the algorithm(or the code in GROMACS). Thanks. Gu

[gmx-users] which charge is used in gromacs program

2011-08-31 Thread GZ Zhang
Hi, ALL I have a question about the charge defined in the topology file. It seems to me that the charge for each atom apprears twice in different sections of the topology files. -- One is [ atomtypes ] ;n

[gmx-users] initial temperature ridiculously high

2011-06-15 Thread GZ Zhang
Hi, ALL I met a bizarre in a NVT simulation in which the initial temperature is ridiculously high. Even though I specify the initial temperature to be 200 K. ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 200.0 gen_seed = 173529 En

[gmx-users] what is the "nicelevel" ?

2010-12-07 Thread GZ Zhang
Hi, ALL I'm using "genbox" to create a water box. There is a flag called "-nice" which is described to be used to set the nicelevel. What is nicelevel ? What does the default value "19" mean ? What if I would like to increase the decimal places (the default is 3) of all numbers. Thanks.

[gmx-users] How to add NaCl to bulk liquid water

2009-12-09 Thread GZ Zhang
Hi, All Given the configuration file of a bulk SPCE water system, how can I add a Na+ and Cl- into it using some gromacs or vmd tool? I tried autoionize tool in vmd, but failed due to no psf file; then I tried autopsfgen tool, failed again due to no proper topology file that can recognize SPC