[gmx-users] Exploding box after 55.5ns of simulation

= -1 constraints = hbonds Thank you, JW -- JW Feng Ph.D. Candidate Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please sea

Re: [gmx-users] t-couple warning

>From reading the wiki, it seems like it is better to couple the entire system to one thermostat. Would this better? tc_grps = system Thanks, JW On 10/11/07, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting JW Feng <[EMAIL PROTECTED]>: > > > H

[gmx-users] t-couple warning

Hello, This is a new warning that appears when executing version 3.3.2 of grompp to create a .tpr file. Should I be concerned? WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group PROTEIN has fewer than 10% of the atoms (504 out of 24494) Maybe you want to try Protein and Non-Protein

[gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem

Using "trjconv -ur compact -pbc atom" worked. JW On 10/9/07, JW Feng <[EMAIL PROTECTED]> wrote: > GMX users, > > In 3.3.1, I used "trjconv -ur compact -pbc whole " to convert a > rhombic dodecahedron box so it could be displayed properly in VMD. > Th

[gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem

GMX users, In 3.3.1, I used "trjconv -ur compact -pbc whole " to convert a rhombic dodecahedron box so it could be displayed properly in VMD. This does not appear to be working in 3.3.2. Is there another way to convert a box so it displays properly in a visualization program? This is the comman

Re: [gmx-users] solubility of PVME in TIP5P

Did you noticed that the number of TIP5P water molecules is about half of what's needed to fill the box. I think that's why your box collapsed. JW On 4/23/07, kitty ji <[EMAIL PROTECTED]> wrote: > > > > > Dear GMX user, > > > > Explicated model of Poly (vinyl methyl ether) was built with ether >

Re: [gmx-users] genbox using tip5p water results in too few number of water molecules

7, David van der Spoel <[EMAIL PROTECTED]> wrote: > JW Feng wrote: > > Hello, > > > > I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC, > > TIP4P and TIP5P water with " > > genbox -cs .gro -box 1 1 1". The TIP5P box contains half > >

[gmx-users] genbox using tip5p water results in too few number of water molecules

Hello, I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC, TIP4P and TIP5P water with " genbox -cs .gro -box 1 1 1". The TIP5P box contains half the number of water molecules compared to TIP4P and SPC. SPC: 33 SOL molecules, density=987.205 (g/l) TIP4P: 31 SOL molecules TIP5P: