[gmx-users] angle restraints
hello I want to add angle restraints in my itp file for a ligand. what is the proper way of inserting angle restraint in .itp file ? Is there any keywords I have to add to my .mdp file for angle restraints? I have searched the mail archieve, I found many things about adding dihedral angle restraints but I couldnot find anything about adding angle restrains. Please advice. Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Position restrained Dynamics
Hi All, I am trying to simulate kinase domain (chain A) in complex with cyclin (chain B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need to keep only kinase domain flexible but cyclin fixed. i put POSRES_B in define variable and tried to simulated the entire solvated system in GROMACS 4 package. But time and again it failed with LINCS warnings. On the contrary, if entire system is kept either flexible or position restrained, run is obtained without any errors. I tried 1ns MD. Unable to understand possible reasons. Could anybody help in this regard ? Regards, Nikhil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] combine position restraints and NPT equlibration in membrane
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God We Trust
Hello
Dear GMX users
We would like to perform MD simulation of a protein
in attendance of biomembrane (POPE). On the basis of Kalp tutorial, can we
combine position restraints and NPT equlibration in one phase?. We
attached NPT.mdp in this mail. Please guide us.
Many thanks in
advance for your help and your reply.
Yours truly
Karim Mahnam
Institute of Biochemistry and Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/
npt.mdp
Description: Binary data
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Re: [gmx-users] angle restraints
- Original Message -
From: subarna thakur thakur.suba...@yahoo.co.in
Date: Thursday, June 10, 2010 16:41
Subject: [gmx-users] angle restraints
To: gmx-users@gromacs.org
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hello I want to add angle restraints in my itp file for a ligand. what is
the proper way of inserting angle restraint in .itp file ? Is there any
keywords I have to add to my .mdp file for angle restraints? I have searched
the mail archieve, I found many things about adding dihedral angle
restraints but I couldnot find anything about adding angle restrains.
It's in the manual.
Mark
|
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Re: [gmx-users] combine position restraints and NPT equlibration in membrane
- Original Message -
From: Mahnam mah...@ibb.ut.ac.ir
Date: Thursday, June 10, 2010 18:12
Subject: [gmx-users] combine position restraints and NPT equlibration in
membrane
To: gmx-users@gromacs.org
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p{margin-bottom: 0.15em;margin-top: 0.15em;}body{font-family:arial, helvetica,
sans-serif;font-size:10pt;};
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span.macro, span.macro ul, span.macro div, span.macro p {background :
#CC;} p{margin-bottom: 0.15em;margin-top:
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In God We Trust
Hello Dear GMX users
We would like to perform MD simulation of a protein in attendance of
biomembrane (POPE). On the basis of Kalp tutorial, can we combine position
restraints and NPT equlibration in one phase?. We attached NPT.mdp in this
mail. Please guide us.
NPT equilibration with position restraints is not unreasonable, but if your
density is not correct, then your box needs to change size. Since the
position-restrained component can't change its coordinates much, you'll need to
equilibrate for a while to let other things rearrange around it.
Don't T-couple ions seperately. See
http://www.gromacs.org/Documentation/Terminology/Thermostats
Mark
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[gmx-users] g_rmsf -res
Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. To do so, I need to calculate the average per residue. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf I got the same result, when choosing C-alpha for root mean square calculation. So please can anyone explain how can I get the average per residue over a period of time? Thanks, Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rmsf -res
Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com wrote: Hi Everyone, please I have a question concerning g_rmsf. I need to compare the RMSF from my initial structure to the RMSF of my average structure. Single structures (initial c.q. average) do not have an RMSF. When I did g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf or g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -res -o rmsf This is not what you did. Please copy/paste command lines. I got the same result, when choosing C-alpha for root mean square calculation. Sure, when selecting C-alphas, averaging the RMSF per residue (sum_over_calphas_in_residue/number_of_calphas_in_residue) will evidently be identical to calculating the RMSF on an atom basis for each Calpha. So please can anyone explain how can I get the average per residue over a period of time? Select 'protein' (and use the -res flag). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Position restrained Dynamics
nikhil damle wrote: Hi All, I am trying to simulate kinase domain (chain A) in complex with cyclin (chain B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need to keep only kinase domain flexible but cyclin fixed. i put POSRES_B in define variable and tried to simulated the entire solvated system in GROMACS 4 package. But time and again it failed with LINCS warnings. On the contrary, if entire system is kept either flexible or position restrained, run is obtained without any errors. I tried 1ns MD. Unable to understand possible reasons. Probably by restraining whatever configuration you're starting with, you're preserving some unresolved clashes in the system. By either restraining both chains or allowing both to move, you are overcoming the problem. Could anybody help in this regard ? Watch the trajectory to see what's going on. A few other general tips: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin Regards, Nikhil -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problems when using command trjconv
Dear All: I encounter some problems when I am using command trjconv to remove the periodic boundary condition. I am doing molecular dynamics simulations of a pentamer, and some of the subunits jump from one box to its adjacent one. Thus, I try to remove the periodic boundary conditions by trjconv command.The commands I used are as follows: trjconv -s trpfile -f xtcfile -o new_xtcfile -n index.ndx -pbc nojump In the results I found the five subunits are put together to form the initial pentamer which is what I expected. However, I also found some of the subunits are cut off a part (i.e., the subunit is broken into one large piece and several small pieces, the large piece forms pentamer with other subunits, and the small pieces distribute in the boundary of the box). Then, I try to solve this problem by using the follow command: trjconv -s trpfile -f new_xtcfile_lastCommand -o another_new_xtcfile -n index.ndx -pbc whole this time, the subunits are not broken, but the pentamer is not formed(i.e., some subunits in one box and some in the adjancent one). Thus, I am writing to find a way in order to remove the periodic boundary condition and put the subunits together as a pentamer with out break a seperate subunit into several parts.Could anyone be so kind to give me some suggestions? Thank you very much for your insight. Best Wishes R-X Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problems when using command trjconv
mirc...@sjtu.edu.cn wrote: Dear All: I encounter some problems when I am using command trjconv to remove the periodic boundary condition. I am doing molecular dynamics simulations of a pentamer, and some of the subunits jump from one box to its adjacent one. Thus, I try to remove the periodic boundary conditions by trjconv command.The commands I used are as follows: trjconv -s trpfile -f xtcfile -o new_xtcfile -n index.ndx -pbc nojump In the results I found the five subunits are put together to form the initial pentamer which is what I expected. However, I also found some of the subunits are cut off a part (i.e., the subunit is broken into one large piece and several small pieces, the large piece forms pentamer with other subunits, and the small pieces distribute in the boundary of the box). Then, I try to solve this problem by using the follow command: trjconv -s trpfile -f new_xtcfile_lastCommand -o another_new_xtcfile -n index.ndx -pbc whole this time, the subunits are not broken, but the pentamer is not formed(i.e., some subunits in one box and some in the adjancent one). Thus, I am writing to find a way in order to remove the periodic boundary condition and put the subunits together as a pentamer with out break a seperate subunit into several parts.Could anyone be so kind to give me some suggestions? Thank you very much for your insight. Another option is to choose a residue near the central interface of the pentamer and assign it to an index group, then use trjconv -center (choosing this residue as the group to center). -Justin Best Wishes R-X Gu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problems when using command trjconv
On Jun 10, 2010, at 4:54 PM, mirc...@sjtu.edu.cn wrote: Dear All: I encounter some problems when I am using command trjconv to remove the periodic boundary condition. I am doing molecular dynamics simulations of a pentamer, and some of the subunits jump from one box to its adjacent one. Thus, I try to remove the periodic boundary conditions by trjconv command.The commands I used are as follows: trjconv -s trpfile -f xtcfile -o new_xtcfile -n index.ndx -pbc nojump If this command does not work that means your tpr file (reference structure) contains broken subunits. Check it and give a tpr with the subunits full and it will work ... In the results I found the five subunits are put together to form the initial pentamer which is what I expected. However, I also found some of the subunits are cut off a part (i.e., the subunit is broken into one large piece and several small pieces, the large piece forms pentamer with other subunits, and the small pieces distribute in the boundary of the box). Then, I try to solve this problem by using the follow command: trjconv -s trpfile -f new_xtcfile_lastCommand -o another_new_xtcfile -n index.ndx -pbc whole this time, the subunits are not broken, but the pentamer is not formed(i.e., some subunits in one box and some in the adjancent one). Thus, I am writing to find a way in order to remove the periodic boundary condition and put the subunits together as a pentamer with out break a seperate subunit into several parts.Could anyone be so kind to give me some suggestions? Thank you very much for your insight. Best Wishes R-X Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] generation of bilayer structures
Hi all. I am trying to build up a bilayer consisting of a lipid (i.e. DMPC) and a fatty acid. Although I've seen some biblio related with this topic, the methodology about how to insert the fatty acid chain into an equilibrated bilayer is not so clear for me. In J. Phys. Chem. B 2009. 113, 92-102, it is suggested that the fatty acid chains could be inserted using tlc scripting withing VDM, but no clue about the insertion algorithm itself. So I tried the following (using fortran code): first locate the best positions to place the fatty acid chain and subsequently placing them and expanding the cell a bit (by a factor of 1.2) to ensure place enough for the inserted chains. Then the are rotated along z-axis to find the best orientation. Subsequent minimization, solvation and equilibration (NPT) should yield an optimal starting structure for production, but I am not entirely satisfied with the result (sometimes it works, sometimes the systems crashes mainly due to problems during communication between nodes). So I wonder if someone of you has an idea about an efficient way to generate lipid bilayers that may work for my problem. In addition, I would like to know how Gromacs handles the coordinates out of the simulation box in the .gro file during a simulation. I guess it just replicate the coordinates inside the box by the opposite face (using PBC) but I would like to have comment about it if you know. Thanks a lot! Javier -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS on CYGWIN
Dear all, I was wondering whether GROMACS on CYGWIN is less capable than GROMACS run on LINUX? i.e. concerning its speed and its ability to simulate larger macromolecules. I assume that it is faster, but is it very much different? I would be very grateful for your help. Thank you, Nasim -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on CYGWIN
- Original Message -
From: Nasim Biglari nasim...@yahoo.co.uk
Date: Friday, June 11, 2010 2:51
Subject: [gmx-users] GROMACS on CYGWIN
To: gmx-users@gromacs.org
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Dear all,
I was wondering whether GROMACS on CYGWIN is less capable than GROMACS run on
LINUX?
i.e. concerning its speed and its ability to simulate larger macromolecules.
I assume that it is faster, but is it very much different?
GROMACS will run fine, and do approximately the same under either OS on
comparable hardware with the same version of gcc, however for production
simulation to be maximally effective you need to arrange for the simulation
process not to be interrupted much. This is easier to arrange on Linux than
Windows. You certainly don't want to be concurrently using either kind of
machine as a desktop, and also you'd prefer not to be logged on to either
machine.
Mark
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[gmx-users] question about how to install g_tune_pme
Hi, Everyone, We want to install g_tune_pme tool to our Gromacs-4.0.7 on our cluster. We don't know which Makefile in the template directory we should use, should we run make in the tune directory, or even configure, or should we compile this together with gromacs? Should we use mpi library? which one?Thanks a lot. Yi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
