Re: [gmx-users] problem with dimer simulation !
try - cluster, and then as cluster group protein.Kay.On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote: hi, all user: i performed the dimer simulation, and want to realize the interaction between two peptides. but frequently, i encountered this kind of problem: sometimes peptides moved out of the box, and sometimes they jumped back. i have tried so many way to pull them back with trjconv command, but still cause some unexpected problem. for example, peptides break to many parts ( with -pbc whole ) or diffuse out of box gradually ( with -pbc nojump ) with -ur or -center still not the trajectory i really want. i think maybe there are some tricks to perform. any suggestions for me ? thanks sooo much!___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] center of mass pulling in AFM
We have a complex with two chains. From one chain (chain A), we are fixing the COM. We are pulling on the COM of the other chain (chain B). Now assume that due to interactions with chain B, chain A is elongated in the direction of pulling. This means that the COM of chain A has moved in the directions of chain B. To keep the COM of chain A at the same position, the 'rear end' of chain A has to go in the opposite direction than the 'front end', so that chain A experiences additional forces and is even more (and now not due to 'real' interactions, but artificially ) elongated due to the COM fixing. Did I understand that correctly? Thanks, Kay. On Jul 18, 2006, at 11:31 AM, Berk Hess wrote: From: Kay Gottschalk [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: [gmx-users] center of mass pulling in AFM Date: Mon, 17 Jul 2006 12:58:02 +0200 Hi there, we are doing pulling simulations of protein complexes. For these simulations, we keep the COM of one group fixed and pull on the COM of the other group. Now we got into this discussion, whether this introduces artificial distortions on the hold protein. If the protein deforms into the direction of the force vector, the center of mass changes. Does this mean that a force on the other end of the protein is applied, so that the other end also deforms in order to keep the center of mass fixed? Or how is the COM held fixed ? This all depends on what you are keeping fixed. Of which groups are you keeping the COM fixed? Since MD preserves momenta, you can only fix distances between COMs by adding forces, which is exactly what the pull code does. Additionally fixing more than one COM will introduce additional forces. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] center of mass pulling in AFM
Thanks for your suggestion to do something more similar to reality. We are trying to mimick an experiment with covalently bound protein. Of course the protein is not fixed in the center of mass, but at some sidechain. Now due to all kind of effects, if we simulate with this sidechain atom fixed, the protein unfolds. This is mainly caused by the sad fact that our simulations still cannot span the time scale of the experiment. Too bad. Therefore, we need to find some way around this problem. Since the unfolding has something to do with a combination of force propagation and viscous drag, it might be more similar to the experiment to pull at the center of mass than at one atom. This is when our discussion about COM started. You see, we are indeed trying to simulate something more similar to reality. Thanks again for your comments, Kay. On Jul 18, 2006, at 3:39 PM, Berk Hess wrote: From: Kay Gottschalk [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] center of mass pulling in AFM Date: Tue, 18 Jul 2006 14:41:53 +0200 Ok, that's what we thought. So would you think that it is a better idea to fix an atom close to the center of mass instead of the center of mass itself? That way, one shouldn't get any additional forces acting on the rear end, just forces acting on a single atom in the center. Would you agree with that? Indeed. But fixing a single atom is space is quite an unrealistic situation, unless you are trying to mimick something like an experiment where a protein is covalently bound to a surface. It all depends on what you want to do. There is probably some kind of experiment or biological process that you are trying to mimick. Doing something more similar to reality should reduce your problems. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] center of mass pulling in AFM
Hi there, we are doing pulling simulations of protein complexes. For these simulations, we keep the COM of one group fixed and pull on the COM of the other group. Now we got into this discussion, whether this introduces artificial distortions on the hold protein. If the protein deforms into the direction of the force vector, the center of mass changes. Does this mean that a force on the other end of the protein is applied, so that the other end also deforms in order to keep the center of mass fixed? Or how is the COM held fixed ? Best, Kay. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] To add all hydrogens
Depends on the force field. Take opls/aa for all hydrogens.Best,Kay.On May 22, 2006, at 3:52 PM, [EMAIL PROTECTED] wrote:Dear All, First of all, I would like to give my thanks for the help David van der Spoel has given us. I'm doing an energy minimization with mdrun without problems. However, I've noticed that Gromacs is only adding the polar hydrogens and not all the hydrogens during the energy minimization. I would like to know if GROMACS is able to add all hydrogens and what I have to do, which option I have to choose if it is possible. Thanks in advance for your help. Regards, Montserrat ___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ~~Dr. Kay-Eberhard GottschalkApplied Physics and Center for Nano SciencesLudwig-Maximilians UniversityAmalienstr. 5480799 Munich, GermanyPhone: +49-89-2180 3436 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist
They are not interacting. The distance is larger than 40 Å. But still,if the distance to the mirror image is 41 Å and to the same protein in the box is 45 Å, the distance to the mirror image will be plotted... We are indeed pulling on z. Best, Kay. On May 22, 2006, at 6:02 PM, Xavier Periole wrote: Kay Gottschalk wrote: Hi there, we are doing a pulling simulation and want to monitor the distance between two atoms during pulling. Using g_dist the distance is calculated between all mirror images of the periodic boundary conditions, and the minimal distance is calculated. In our case, this is uncomfortable, since the distance should be monotonically increasing, but since after approximately half of the simulation one atoms starts to become closer to the mirror image in the next box, it looks as if the distance is decreasing. Is it possible to switch off the pbc condition in g_dist? I didn't find it in the manual or the user list. Is it any good to have your two atoms interacting through the images ?? It does not sound too good to me ... You can just plot the distance and the size of the box (g_energy give the box size) and then just substract the corresponding dimension if the box to the distance you obtained with g_dist. I guess your are pulling on one of the axes !!! XAvier -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-page: http://md.chem.rug.nl/~periole -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ~~ Dr. Kay-Eberhard Gottschalk Applied Physics and Center for Nano Sciences Ludwig-Maximilians University Amalienstr. 54 80799 Munich, Germany Phone: +49-89-2180 3436 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_dist
I can also use VMD - not quite as comfortable as g_dist with the pbc problem solved, but probably the quick and dirty 'fix', since I will have to look at the trajectories anyway. Thanks, Kay. On May 22, 2006, at 6:27 PM, Alan Dodd wrote: That'd certainly work if the movement is continuous, but if there are many fluctuations near the crossover point then sorting out which steps to fudge it at could be a pain. Assuming you only care about the Z seperation, I'd be tempted to use g_traj to plot both groups, and subtract the z-position of one group from the other at each step. Just a thought. --- Xavier Periole [EMAIL PROTECTED] wrote: Kay Gottschalk wrote: They are not interacting. The distance is larger than 40 Å. But still,if the distance to the mirror image is 41 Å and to the same protein in the box is 45 Å, the distance to the mirror image will be plotted... We are indeed pulling on z. Best, Kay. Good, so the solution I proposed should solve your problem !! XAvier -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-page: http://md.chem.rug.nl/~periole -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ~~ Dr. Kay-Eberhard Gottschalk Applied Physics and Center for Nano Sciences Ludwig-Maximilians University Amalienstr. 54 80799 Munich, Germany Phone: +49-89-2180 3436 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rdf on Mac OS X 10.3, 10.4
| PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
fnTPS = ftp2fn_null(efTPS,NFILE,fnm);
fnNDX = ftp2fn_null(efNDX,NFILE,fnm);
/* bSQ = opt2bSet(-sq,NFILE,fnm) || opt2parg_bSet(-grid,NPA,pa); */
bSQ = opt2bSet(-sq,NFILE,fnm);
bRDF = opt2bSet(-o,NFILE,fnm) || !bSQ;
if (bSQ) {
if (!fnTPS)
fatal_error(0,Need a tps file for calculating structure factors\n);
}
else {
if (!fnTPS !fnNDX)
fatal_error(0,Neither index file nor topology file specified\n
Nothing to do!);
}
if (bSQ)
do_scattering_intensity(fnTPS,fnNDX,opt2fn(-sq,NFILE,fnm),ftp2fn(efTRX,NFILE,fnm),
start_q, end_q, energy );
/* old structure factor code */
/*do_sq(fnNDX,fnTPS,ftp2fn(efTRX,NFILE,fnm),opt2fn(-sq,NFILE,fnm),
ftp2fn(efXPM,NFILE,fnm),grid,lambda,distance,npixel,nlevel);
*/
if (bRDF)
do_rdf(fnNDX,fnTPS,ftp2fn(efTRX,NFILE,fnm),
opt2fn(-o,NFILE,fnm),opt2fn_null(-cn,NFILE,fnm),
opt2fn_null(-hq,NFILE,fnm),
bCM,cutoff,binwidth,fade);
thanx(stderr);
return 0;
}
On May 4, 2006, at 9:50 PM, David van der Spoel wrote:
Jennifer Rendell wrote:
Dear friends,
I have seen a couple of postings (January 2004, gmx-developers,
David Bostick, and November 2003, gmx-users, Kay Gottschalk) on
segmentation faults from g_rdf on Mac OS X systems.
I am using the Getting Started section of the gromacs web
pages, in particular, the section on water, where the command
g_rdf is called.
Below I show the results from two versions of gromacs, 3.2.1 on a
Mac OS X 10.4, and 3.1.5_pre2 on a Mac OS X 10.3. The results are
similar in that each results in a segmentation fault. g_rms and
gmxcheck work as I expect.
Any ideas on how to fix this? Jennifer
Maybe you don't want to hear this, but please upgrade to 3.3.1 and
try again. If the problem persists in the latest version please
post a bugzilla.
*
** 1. gromacs 3.2.1 on Mac OS X 10.4 (Tiger). g_rdf gives
the following
results:
% g_rdf -f water.trr -n oxygen.ndx -o rdf.xvg -s water.tpr
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 3.2.1 (-:
(deleted some lines)
:-) g_rdf (-:
Option Filename Type Description
-f water.trr InputGeneric trajectory: xtc trr trj
gro g96 pdb
-s water.tpr Input, Opt! Structure+mass(db): tpr tpb tpa
gro g96 pdb
xml
-n oxygen.ndx Input, Opt! Index file
-ordf.xvg Output, Opt! xvgr/xmgr file
(deleted all remaining option lines)
Reading file water.tpr, VERSION 3.2.1 (single precision)
Reading file water.tpr, VERSION 3.2.1 (single precision)
How many groups do you want to calculate the RDF of?
1
Select a reference group and 1 group
Group 0 ( OW) has 216 elements
There is one group in the index
There is one group in the index
trn version: GMX_trn_file (single precision)
Last frame 10 time 10.000
Segmentation fault
*
** 2. gromacs 3.1.5_pre2 on Mac OS X 10.3 (Panther). g_rdf
gives the
following results (which appear to be the same as the above):
$ g_rdf -f water.trr -n oxygen.ndx -o rdf.xvg -s water.tpr
:-) G R O M A C S (-:
Go Rough, Oppose Many Angry Chinese Serial killers
:-) VERSION 3.1.5_pre2 (-:
(deleted some lines)
:-) g_rdf (-:
Option Filename Type Description
-f water.trr Input Generic trajectory: xtc trr trj
gro g96 pdb
-s water.tpr Input, Opt! Structure+mass(db): tpr tpb tpa
gro g96 pdb
-n oxygen.ndx Input, Opt! Index file
(deleted all remaining option lines)
Reading file water.tpr, VERSION 3.1.5_pre2 (single precision)
Reading file water.tpr, VERSION 3.1.5_pre2 (single precision)
How many groups do you want to calculate the RDF of?
1
Select a reference group and 1 group
Group 0 ( OW) has 216 elements
There is one group in the index
There is one group in the index
trn version: GMX_trn_file
Last frame 10 time 10.000
Segmentation fault
*
** ___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
