[gmx-users] viewing .xvg plots in windows environment

Hi, I am trying to view my GROMACS ".xvg" outputs (2D plots) in windows XP environment. Can anyone please suggest a good way to do this? -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] energy minimization using double precision gromacs failed

Hello, gmx-users,I tried to energy minimize a lipidbilayer consisting of 32 lipids(16 up and 16 down) with two water layers(428 up and 428 down). my em.mdp is like this: title= cpp = /lib/cpp include = define = -DFLEXIBL

Re: [gmx-users] viewing .xvg plots in windows environment

Terry Nelson wrote: Hi, I am trying to view my GROMACS ".xvg" outputs (2D plots) in windows XP environment. Can anyone please suggest a good way to do this? http://wiki.gromacs.org/index.php/Graphing_Data Mark ___ gmx-users mailing listgmx-user

Re: [gmx-users] viewing .xvg plots in windows environment

You can easily import the xvg file in excel or any other program of the same kind Regards, Eric Terry Nelson wrote: Hi, I am trying to view my GROMACS ".xvg" outputs (2D plots) in windows XP environment. Can anyone please suggest a good way to do this? -- Cheers, Terry --

Re: [gmx-users] energy minimization using double precision gromacs failed

There's probably a problem either with your structure or your topology. Spend some time looking at what you've done. I'd start by investigating atom 483. It should be pretty obvious what's wrong, with a force like that. - Original Message From: Q733 <[EMAIL PROTECTED]> To: gmx-users@

Re: [gmx-users] viewing .xvg plots in windows environment

Hi, On Monday, 13. August 2007 10:47, Terry Nelson wrote: > Hi, > > I am trying to view my GROMACS ".xvg" outputs (2D plots) in windows XP > environment. Can anyone please suggest a good way to do this? Use the option -noxvgr -[no]xvgr boolyes Add specific codes (legends etc.) in the o

[gmx-users] RE: problems with parallel mdrun

Dear Mark and Carsten, Thanks for the reply Manually setting the grid dimensions works but I have a doubt Since I am using walls in my simulations with wall_ewald_zfac =3 Will it be more appropriate to use Fourier_nx=52 Fourier_ny=52 Fourier_nz=156 Or to leave Fourier_nz=52 and grompp will exten

[gmx-users] GROMACS vs. AMBER speed comparison?

Hi, gmx-users, Recently I have try to use AMBER 9 for the simulation of protein with about 300 residues. Surprisingly, I found that AMBER is far slower than GROMACS; GROMACS is about twice faster. I can not figure out the reason. Why is GROMACS faster than AMBER? Could anybody know the reason? Or

Re: [gmx-users] energy minimization using double precision gromacs failed

Hi, How about trying md with very small step size such as dt = 0.0001 ? Once I had similar problem like you and it is solved by performing additional energy minimization step with very small step size. I can't guarentee this method, but I think it might be OK. On 8/13/07, Q733 <[EMAIL PROTECTED

Re: [gmx-users] GROMACS vs. AMBER speed comparison?

It is found on Gromacs' website http://www.gromacs.org/content/view/12/176/ Regards, Yang Ye - Original Message From: SeungPyo Hong <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, August 13, 2007 9:12:47 PM Subject: [gmx-users] GROMACS vs. AMBER speed comparison? Hi, gmx-

[gmx-users] how to build up fixed connections? how to simulate no electrostatics?

Hey everybody. I'm still trying to biuld up a bulk of 2CLJ-molecules (ethane). I just wanna use fixed connections in-between the CH3-"atoms" and no eletrostatics during the simulation. I posted my .itp-file several times along my .top-file and my used .mdp-file. Though the simulation runs fine

[gmx-users] Principal Component Analysis

Hello, I have a question concerning principal component analysis. In principal component analysis (PCA) it is assumed that the coordinates along each degree of freedom are Gaussianly distributed. If the data does not follow a normal distribution, PCA may not identify the correct principal modes s

[gmx-users] stepsize too small

Hi, This is the first time I`m using gromacs. That`s why I`m having a beginners`question. I tried to do an energy minimization, but after 45 steps this message appears and I know that the following lines have led to questions before: "Stepsize too small (9.09769e-007 nm)Converged to machine p

Re: [gmx-users] stepsize too small

Hello! There are many discussions on the maillist about this... In short, if all you want to do is normal md, it should be ok to just proceed with that. Just check that your potential energy is negative and everything should fine. Otherwise, recompiling Gromacs to use double precision migh

[gmx-users] configure: Unknown floating-point format w/IRIX?

A build on IRIX 6.5.30m with cc version 7.3.1.3m, using -n32 -mips4, gives the following error: checking floating-point format... configure: WARNING: Unknown floating-point format It does correctly figure out that the format is big-endian: checking whether byte ordering is bigendian... (cached

Re: [gmx-users] configure: Unknown floating-point format w/IRIX?

In message <[EMAIL PROTECTED]> (on 13 August 2007 17:12:41 -0400), [EMAIL PROTECTED] (Allen Smith) wrote: > >A build on IRIX 6.5.30m with cc version 7.3.1.3m, using -n32 -mips4, gives >the following error: > >checking floating-point format... configure: WARNING: Unknown floating-point >format > >I

[gmx-users] version 3.3.1 .tpr file with version 3.2 g_order

The g_order tool in gromacs 3.3.1 is broken. I know that there is a patch available that would fix it, but a colleague advised me that recompiling g_order would not be quick and easy. I therefore thought that I might use g_order from gromacs 3.2, but it complains of a version 3.3.1 ru

[gmx-users] Long-term drift, crash

Hi, I have been struggling for some time with a nasty problem with my simulations of RNA in water using Gromacs 3.3.1 and the AMBER ports. Nobody ever reported it so I am afraid I did some obvious mistake that I just cannot see. After some steps (between 5 and 15), my simulations crash,

Re: [gmx-users] Principal Component Analysis

On Mon, 13 Aug 2007, Matthias Waegele wrote: Hello, I have a question concerning principal component analysis. In principal component analysis (PCA) it is assumed that the coordinates along each degree of freedom are Gaussianly distributed. If the data does not follow a normal distribution, P