[gmx-users] g_rmsdist error hi (-1000.000000) <= lo (0.000000)

r: hi (-1000.00) <= lo (0.00) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Could you please help me? Thanks Andrea -- ¯¯¯¯ Andrea Carotti Dipartimento di Chimica e Tecnologia del

[gmx-users] g_sas with pbc

Hi all, I've already simulated 27 organic molecules in a cubic solvent box. Now I would like to calculate the SAS of this system. I've a tpr and a trr with only the molecules inside (without water). I'm using gromacs 4.0.5. I've added the box dimension infos to the trr using the command: trjconv -f

[gmx-users] Variance in ED

Dear Dr. Wassenaar, many thanks for your kind reply. Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www

[gmx-users] Variance in ED

Hi all, perhaps a silly question but i didn't find the correct way to calculate the variance explained by each eigenvec in ED analysis. Could someone point me out to a correct tool/option to use. I'm using gmx v3.3. Many thanks Andrea -- ¯¯¯¯¯¯¯¯ Andrea Carotti Dipar

[gmx-users] xpm to ascii

Hi all, I would like to have a txt file from an xpm matrix generated by g_rms or g_cluster. Someone has already done this? I've seen in the previous posts some hints about hacking the code or scripts usefull for g_covar...but I'm not so confortable and expert to do such things without a step by ste

Re: [gmx-users] g_rms

> So does the -Rmat option not produce a human-readable text file? Hi, unfortunately I can't see this option in g_rms. I'm using the v 3.3.1 and also on the reference page online there is not -Rmat. Am i missing something? Thanks Andrea ___ gmx-users ma

Re: [gmx-users] g_rms

-f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin I obtain a rmsd.xvg with 2 columns. So, which is the meaning of that value? a mean of all the rmsd calculated for that frame in respect to the other 33 refs? Thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Te

Re: [gmx-users] g_rms

Hi, > You should be getting such a 2200x33 matrix. My guess is that the > command line or files that you're using are not what you think they > are :-) my command line is g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin Note that the pdbs (traj and ref) have the same number of atoms (same

[gmx-users] g_rms

Hi and thanks for answering to my previous question. Now I'm calculating the rmsd between two trajectories (-f2 option). One is made by 2200 frames and the other has 33 frames..Now I've some doubt about the output (rmsd.xvg), cause this file has only two columns with 2200 rows ...i was imaging that

[gmx-users] g_cluster questions

, but it asks me however for a group for the LSfitting..could someone explain me this behaviour? Is my procedure correct for my purpose? Is normal that g_cluster does not accept the -fit option? Thanks Andrea -- ¯¯¯¯¯¯¯¯ Andrea Carotti Dipartimento di Chimica e Tecnologia del

[gmx-users] psf 2 top

Hi all, I've performed my MD simulations using the charmm FF and NAMD (so pdb,psf and dcd files). Now i would like to use the great GMX analysis tools. I've successfully converted the dcd file in trr (using catDCD). Now the next step I'd like to do is the psf to top conversion. I've seen on the vmd

[gmx-users] g_hbond -contact option

Hi all, I have found this interesting option in g_hbond, and I would like to know something more about it. How does it work? Which is the difference with other tools like g_dist? Thanks to all Andrea ___ gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] Re: g_hbond error "Your computational box has shrunk too much"

The problem is that i don't have an energy file cause this time I'm using gromacs only for analyze my trajs...so I don't know how to make the plot you suggested. Now perhaps I've found a workaroud using trjconv with the option -box 1 1 1 set, but I' don't know if this could be correct. (I've checke

[gmx-users] Re: g_hbond error "Your computational box has shrunk too much"

> Is it correct? Did you plot the box volume as a function of time? > You can use g_hbond for different stretches of the trajectory and > combine the results manually. > -- Thanks for the fast reply. I'm only trying to monitor the hbond formation with the " basic" command g_hbond -f m93_newtraj.t

[gmx-users] g_hbond error "Your computational box has shrunk too much"

Hi all, I'm beginning to analyze my trajectories, everything works fine with (g_rmsf, g_saltbr ...) but when i try to use g_hbond I receive this error: -- Program g_hbond, VERSION 3.3.1 Source code file: gmx_hbond.c, line: 631 Fatal error: Your computational box has shrunk too much. g_

[gmx-users] Reordering problem AMBER to GROMACS

Hi all gmxers, I'm trying to analyze an amber dynamic (v.8) with the gromacs tools (last version). Sorry in advance for the long message. To do so, I'm trying to generate also a tpr file (needed by some tools). My procedure is being to convert all the MD in multiple pdb format. So I have extracted

Re: [gmx-users] Paralellization limit?

From: "Carsten Kutzner" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Wednesday, April 19, 2006 2:15 PM Subject: Re: [gmx-users] Paralellization limit? Hi Andrea, Andrea Carotti wrote: Hi all, I'm trying to simulate a system with two identical pr

[gmx-users] Paralellization limit?

Hi all, I'm trying to simulate a system with two identical proteins (42aa each one), solvent spc (18430 mols) and 6 ions NA+...for a total of ~56100 atoms. Now the "problem" is that if I run the MD on 4 nodes everything works fine, but when I try to use 6 or 8 cpus the process stops on the mast

Re: [gmx-users] replica exchange doubt

Hi all, I've another question, in the manual (page 39) a REMD calculator is mentioned. Where is it? I've tried to search it on the website without success. Thanks again Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.

Re: [gmx-users] replica exchange doubt

Thanks to all for the quick clarifications. Andrea - Original Message - From: "Xavier Periole" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Tuesday, April 11, 2006 1:55 PM Subject: Re: [gmx-users] replica exchange doubt Andrea Carotti

[gmx-users] replica exchange doubt

Hi all gmx-ers, I have a doubt concerning the REMD setup. Let's say I want to use 12 cpus to make a REMD at 2 different temp 300 and 400K of the same system. Should I prepare every tpr file with the -np option set to 6? and then run the mdrun with -np 12 -multi -s 300.tpr 400.tpr -replica X -re

Re: [gmx-users] How to install MPI version of Gromacs on a Linux Cluster

Hi, Here http://www.gromacs.org/documentation/howtos/mpich_howto.html you'll find an interesting solution for you.. Bye Andrea - Original Message - From: "Shankar Prasad Kanaujia" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Cc: Sent: Monday, March 27, 2006 8:03 AM Subject: [gmx-users]

[gmx-users] AFM pulling

Hi all, I am a bit confused about some points on the manual (section 6.1, manual 3.2). I f i define two groups: one that will be pulled and the other as reference group; then the force constant and the rate, must i define also the afm_dir and the afm_unit? In my mind, if i define two groups (ce

Re: [gmx-users] Gromacs 3.3 manual

-users] Gromacs 3.3 manual Andrea Carotti wrote: Hi all, I'm trying to create the manual from the cvs repository suing the command: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co manual and then using the README file on that dir created. But I'm encountering a lot of errors a

[gmx-users] Gromacs 3.3 manual

Hi all, I'm trying to create the manual from the cvs repository suing the command: cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co manual and then using the README file on that dir created. But I'm encountering a lot of errors and problem ending with a creation of an unreadable pdf. I'm u