[gmx-users] Is gromacs-4.0.2 finally released?

Hi all, I found that gromacs-4.0.2.tar.gz under ftp.gromacs.org/pub/gromacs for a while, but now it is no longer there. Is this version finally and officially released? Regards, Jian ___ gmx-users mailing listgmx-users@gromacs.org http://www.groma

[gmx-users] atom name in pdb converted by editconf (gmx4)

Hi, I found that when the output format from editconf (gmx4) is PDB, atom name like H5'1 will be changed to 1H5'. For other four-character atom name like ABCD, editconf works properly. example: editconf -f a.pdb -o b.pdb = a.pdb == ATOM 1 PDT 1 -1.84

[gmx-users] m) Re: modify bondfree.c and recompile

n list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Jian Zou wrote: >> Hi Mark, David and Bess, >> >> Thank you all for the suggestions. >> >> >> I know the dependency has to be s

[gmx-users] Re: modify bondfree.c and recompile

ed, 22 Oct 2008 11:57:46 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] modify bondfree.c and recompile > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > >

[gmx-users] modify bondfree.c and recompile

Hi, If I only change some functional form in bondfree.c (the number of parameters are kept the same), can I just do "make mdrun" and "make install-mdrun" to recompile from the source? I cannot find the dependency between the source files and the Gromacs utilities (grompp and mdrun). I compare th

[gmx-users] Howto output from bondfree.c

Hi all, I am trying to modify the functional form of a bonding interaction in bondfree.c and how to output from this source file if I want to check the value of some variable? I tried printf or fprintf following fopen, neither works. Any suggestion is highly appreciated. Regards, Jian ___

[gmx-users] Re: gmx-users Digest, Vol 48, Issue 97

Though it is trivial, did you check if mpich/lam/openmpi is compiled by icc and icc in PATH is the one you want? Did you try icc9 and fftw3 and get the same error? Regards, Jian > Message: 7 > Date: Mon, 28 Apr 2008 12:24:04 +1000 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gm

[gmx-users] Re: gmx-users Digest, Vol 48, Issue 67

00 > From: Dechang Li <[EMAIL PROTECTED]> > Subject: [gmx-users] Re: the number of water molecules (Jian Zou) > To: "gmx-users@gromacs.org" > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="gb2312" > > > >

[gmx-users] Re: the number of water molecules

How about using vmd selection "within" to do this > Message: 3 > Date: Sun, 20 Apr 2008 21:01:57 +0800 > From: Dechang Li <[EMAIL PROTECTED]> > Subject: [gmx-users] the number of water molecules > To: "gmx-users" > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="

[gmx-users] Re: g_hbond

Hi David, Thank you for the explanation. Regards, Jian Zou - Original Message - Date: Fri, 11 Aug 2006 08:24:54 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re: g_hbond To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]>

[gmx-users] Re: g_hbond

Hi David, I read your JPCB paper (JPCB-110-4393) and it says that the geometric criteria with DA distance and DHA angle is employed. Therefore I'm a little confused which angle is indeed used to determine the Hbond, HDA or DHA? Regards, Jian Zou David van der Spoel wrote: > De