[gmx-users] Gromacs 4.5.5

Dear All, I've had to re-install my gromacs on my computer and I'm having issues getting past the "Making all in Man7" during the "make" stage. Below (at the end) are 2 copies of different outputs I get during my installation. The first copy is from the "make.log" file. The second copy is from

[gmx-users] Distance.dat file in umbrella sampling

Dear Justin, I am testing a umbrella simulation basing on your tutorial. But after using your distances.pl script, i do not have the file "summary_distances.dat". It only makes many xvg files. I post the script below: #!/usr/bin/perl -w use strict; # loop g_dist command - measure distance in ea

Re: [gmx-users] Distance.dat file in umbrella sampling

On 6/16/13 7:47 PM, Kieu Thu Nguyen wrote: Dear Justin, I am testing a umbrella simulation basing on your tutorial. But after using your distances.pl script, i do not have the file "summary_distances.dat". It only makes many xvg files. I post the script below: #!/usr/bin/perl -w use strict;

[gmx-users] Re: Gromacs 4.5.5

Hi, Alaina Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ? maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-5-5-tp5009198p5009203.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list

[gmx-users] NVT .gro for NPT

Hi, all I run a small peptide, and after NVT, I got the XXX.gro file like this, because the peptide not at the center of box, I use this .gro to run NPT, if it reasonable? If it's not good, how can I avoid such phenomenon? Thank

[gmx-users] a snapshot of NVT

Hi, all When I run a small peptide at NVT stage, I get a snapshot like this: I am not sure if it right, and can I use it for NPT ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.co

Re: [gmx-users] NVT .gro for NPT

Hi Maggin, Why would that be a problem? Tsjerk On Mon, Jun 17, 2013 at 7:28 AM, maggin wrote: > Hi, all > > I run a small peptide, and after NVT, I got the XXX.gro file like this, > > > > because the peptide not at the center of

Re: [gmx-users] a snapshot of NVT

Hi Maggin, Okay, this image may require a bit of explanation :p VMD has drawn bonds according to the bondedness in a reference file. But the atoms have moved, and some went over the box boundaries. So they show up with long bonds crossing the whole box. It's not a problem, just a visualization art

[gmx-users] a snapshot of NVT

Hi, all When I run a small peptide at NVT stage, I get a snapshot like this: I am not sure if it right, and can I use it for NPT ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.co

[gmx-users] Re: NVT .gro for NPT

Hi, Tsjerk You asked me a good question. Ya, sometime it accords my imagination to tell if it right or not. That's not the correct way. Maybe it near boundary, like at the boundary of dangerous. So let me have such question. maggin -- View this message in context: http://gromacs.5086.x6

[gmx-users] Re: a snapshot of NVT

Hi,Tsjerk, Oh, that's it ! Thank you very much for your kind help! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009206p5009211.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@

Re: [gmx-users] Re: Gromacs 4.5.5

On Jun 17, 2013 5:50 AM, "maggin" wrote: > > Hi, Alaina > > Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ? Installing cmake for an autotools build isn't going to help ;-) Mark > > maggin > > > > -- > View this message in context: http://gromacs.5086.x6.nabble.com/Grom