Re: [gmx-users] Why does the -append option exist?

On 5/06/2011 12:31 PM, Dimitar Pachov wrote: This script is not using mdrun -append. -append is the default, it doesn't need to be explicitly listed. Ah yes, very true. Your original post suggested the use of -append was a problem. Why aren't we seeing a script with mdrun -appe

Re: [gmx-users] binaries for mac os x 10.6

On Sun, Jun 5, 2011 at 6:12 AM, wrote: > Dear Users: > > Does somebody have a set of gromacs binaries for mac os X 10.6.7 that they > can post somewhere (perhaps in > http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries)? > > Macbook Air 3.1 > Version 10.6.7 > 1.4 GHz Intel Core 2

Re: [gmx-users] binaries for mac os x 10.6

Hi Chris, I tried to find the Mac version of Gromacs binary a year ago without success. I sticked with the source code and compiled using xcode. It has been good and stable so far on my macbookpro. Sorry for being a no help but perhaps Gromacs developers have something handy and more compact. You

[gmx-users] Why does the -append option exist?

Dear Dimitar: to me, your posts have indeed appeared very aggressive. So much so that there are probably many people who can help who have decided not to bother due to what they perceive your tone to be. On to the problem at hand: I agree with the previous suggestion that you may have som

Re: [gmx-users] Why does the -append option exist?

On Sat, Jun 4, 2011 at 9:09 PM, Mark Abraham wrote: > On 5/06/2011 3:11 AM, Dimitar Pachov wrote: > On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham > wrote: > > On 4/06/2011 8:26 AM, Dimitar Pachov wrote >> >> > Here is an example: > > > [dpachov]$ ll -rth run1* \#run

Re: [gmx-users] Why does the -append option exist?

On 5/06/2011 3:11 AM, Dimitar Pachov wrote: On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham > wrote: On 4/06/2011 8:26 AM, Dimitar Pachov wrote If this is true, then it wants fixing, and fast, and will get it :-) However, it would be surprising for s

Re: [gmx-users] Transition path sampling

Hey, You could use the path collective variables included in PLUMED (you have to compile it with gromacs) or maybe if you know an eigenvector that describes the motion you are interested in (from PCA for instance) you could do some floodin through it. best Felipe Mensaje origina

[gmx-users] Transition path sampling

Hi , I was wondering whether current GROMACS versions can perform transition path sampling to study rare events ? Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Li

[gmx-users] binaries for mac os x 10.6

Dear Users: Does somebody have a set of gromacs binaries for mac os X 10.6.7 that they can post somewhere (perhaps in http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries)? Macbook Air 3.1 Version 10.6.7 1.4 GHz Intel Core 2 Duo 2 GB 1067 MHz DDR3 SMC version 1.67f3 I am t

Re: [gmx-users] Why does the -append option exist?

On Sat, Jun 4, 2011 at 1:50 PM, Rossen Apostolov wrote: > Hi, > > On Jun 4, 2011, at 19:11, Dimitar Pachov wrote: > > By the way, is this ever reviewed: > > "Your mail to 'gmx-users' with the subject > >Re: [gmx-users] Why does the -append option exist? > > Is being held until the list moder

Re: [gmx-users] Why does the -append option exist?

On Fri, 3 Jun 2011 18:26:17 -0400 Dimitar Pachov wrote: > If one uses that option and the run is restarted and is again > restarted before reaching the point of attempting to write a file, > then things are lost, and most importantly, the most important piece > of data, that being the trajectory f

Re: [gmx-users] Why does the -append option exist?

Hi, On Jun 4, 2011, at 19:11, Dimitar Pachov wrote: > By the way, is this ever reviewed: > > "Your mail to 'gmx-users' with the subject > >Re: [gmx-users] Why does the -append option exist? > > Is being held until the list moderator can review it for approval." > This message usually c

Re: [gmx-users] Why does the -append option exist?

By the way, is this ever reviewed: "Your mail to 'gmx-users' with the subject Re: [gmx-users] Why does the -append option exist? Is being held until the list moderator can review it for approval." On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham wrote: > On 4/06/2011 8:26 AM, Dimitar Pachov

Re: [gmx-users] trjconv and g_filter

Yulian Gavrilov wrote: Dear Gromacs users, What type of conversion of coordinates is better to use? I have got 100 ns MD simulations for unmodified ubc7 protein and ubiquitinated ubc7 protein and converted it's trajectories by using trjconv and g_filter: 1.*trjconv* -s md100ns.t

[gmx-users] trjconv and g_filter

Dear Gromacs users, What type of conversion of coordinates is better to use? I have got 100 ns MD simulations for unmodified ubc7 protein and ubiquitinated ubc7 protein and converted it's trajectories by using trjconv and g_filter: 1.*trjconv* -s md100ns.tpr -f traj.xtc -o traj_noPBC_no

Re: [gmx-users] About publication

vidhya sankar wrote: Dear Justin, Thank you for your Immediate reply. now i know How to work in SMD by reading your tutorial .But i need the effective problem to publish in reputed ACS journal. Can you help ME in that aspects?. Through Gmx mail i will contact you for furt

[gmx-users] About publication

Dear Justin,    Thank you for your Immediate reply. now i know How to work in SMD by reading your tutorial .But i need the effective problem to publish in reputed ACS  journal. Can you help ME in that aspects?. Through Gmx mail i will contact you for further proceedings . i hope