Re: [gmx-users] Questions about urea.itp

Lee Soin wrote: Hello! Can the GROMACS topology file urea.itp be used with the OPLS force field? In urea.itp there are two sets of parameters, separated by "#ifdef" directives. Which set should be used? Neither. Check the literature. Thanks! -- SUN Li Department of Physics Nanjing Universit

[gmx-users] Questions about urea.itp

Hello! Can the GROMACS topology file urea.itp be used with the OPLS force field? In urea.itp there are two sets of parameters, separated by "#ifdef" directives. Which set should be used? Thanks! -- SUN Li Department of Physics Nanjing University, China

Re: [gmx-users] viscosity calculation using g_energy (3.3.3)

JMandumpal wrote: Dear GROMACS users, As explained in the manual ( page 139, section 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using g_energy. I opted(40 Mu-X ) from the g-energy selection. But the unit written on the Y axis of the cor

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

Ilya Chorny wrote: Ok, I got it. Set electrostatics to PME-switch. Made rcoulomb-switch .1 less than rcoulomb and set rlist accordingly and now I am conserving energy. Yipee!!! It did not make sense to me that the system had to be fully relaxed to conserve energy. It should conserve energy en

Re: [gmx-users] Height of the box

Look at the last line of your output gro file. It will have the box dimensions. On Wed, Mar 11, 2009 at 10:36 PM, Mark Abraham wrote: > naimah haron naimah wrote: > >> Dear all... >> How to obtain the height of the box after MD simulation finish? This is >> because, during simulation, I didn't p

Re: [gmx-users] Height of the box

naimah haron naimah wrote: Dear all... How to obtain the height of the box after MD simulation finish? This is because, during simulation, I didn't put size of my box. The reason why I didn't put the size because I want put the molecule in random displacement to avoid bottlenecks. So the com

[gmx-users] Height of the box

Dear all... How to obtain the height of the box after MD simulation finish? This is because, during simulation, I didn't put size of my box. The reason why I didn't put the size because I want put the molecule in random displacement to avoid bottlenecks. So the command is editconf -f cat125

[gmx-users] viscosity calculation using g_energy (3.3.3)

Dear GROMACS users, As explained in the manual ( page 139, section 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using g_energy. I opted(40 Mu-X ) from the g-energy selection. But the unit written on the Y axis of the corresponding xvg file

Re: [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION

Jack Shultz wrote: One other question, if GROMACS was compiled with single precision, would that make a difference regarding how well it minimizes a system? A tiny one. The difference is normally only relevant if you're planning a normal mode analysis. Mark __

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

Ilya Chorny wrote: If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE simulation they should counter balance. I am leaking K.E. somewhere. I reran with a relaxed P.E(t) and saw the same behavior. This is happening both at 2 and 4 fs so its not a time step issue. Any thoughts?

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

Ok, I got it. Set electrostatics to PME-switch. Made rcoulomb-switch .1 less than rcoulomb and set rlist accordingly and now I am conserving energy. Yipee!!! It did not make sense to me that the system had to be fully relaxed to conserve energy. It should conserve energy energy as long as it has be

Re: [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION

Thank you, now I'm testing this on a 64 bit, robust linux box. I was using the parameters from this tutorial https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf One other question, if GROMACS was compiled with single precision, would that make a difference regarding how well it mini

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE simulation they should counter balance. I am leaking K.E. somewhere. I reran with a relaxed P.E(t) and saw the same behavior. This is happening both at 2 and 4 fs so its not a time step issue. Any thoughts? I thought it might be

Re: [gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION

Jack Shultz wrote: Has anyone come across this error on a windows platform? Any suggestions? I ran it through a BOINC workunit then tried it stand-alone for troubleshooting. It produces the same result. 23 [main] mdrun 4084 _cygtls::handle_exceptions: Exception: STATUS_ACCESS_VIOLATION 316

Re: [gmx-users] Re: mdrun dies with STATUS_ACCESS_VIOLATION

Jack Shultz wrote: Also the dump file contains this information Exception: STATUS_ACCESS_VIOLATION at eip=0044C09B eax=000533A4 ebx=0045 ecx=000528B4 edx=7F956C88 esi=FD6A65C0 edi=7F5D6C88 ebp=7FB40020 esp=0022AE30 program=C:\Documents and Settings\All Users\Application Data\BOINC\slots\0\

[gmx-users] Re: mdrun dies with STATUS_ACCESS_VIOLATION

Also the dump file contains this information Exception: STATUS_ACCESS_VIOLATION at eip=0044C09B eax=000533A4 ebx=0045 ecx=000528B4 edx=7F956C88 esi=FD6A65C0 edi=7F5D6C88 ebp=7FB40020 esp=0022AE30 program=C:\Documents and Settings\All Users\Application Data\BOINC\slots\0\gromacs\bin\mdrun.exe,

[gmx-users] mdrun dies with STATUS_ACCESS_VIOLATION

Has anyone come across this error on a windows platform? Any suggestions? I ran it through a BOINC workunit then tried it stand-alone for troubleshooting. It produces the same result. 23 [main] mdrun 4084 _cygtls::handle_exceptions: Exception: STATUS_ACCESS_VIOLATION 316870 [main] mdrun 4084

Re: [gmx-users] get a box of 100 molecules

Adrien Delmont wrote: If I create an .rtp file for my molecule how can I use this file when I producing gro and top files and Can I use this .rtp file with oplsaa and gromos 96 force fields for two different md run successfuly ? Because I plan to run md simulations for all atom and united ato

Re: [gmx-users] get a box of 100 molecules

If I create an .rtp file for my molecule how can I use this file when I producing gro and top files and Can I use this .rtp file with oplsaa and gromos 96 force fields for two different md run successfuly ? Because I plan to run md simulations for all atom and united atom force fields and compar

Re: [gmx-users] phi / psi values using g_chi

Your answer was very useful! I actually could point out where the "confusion" came from! Thanks, XAvier. On Mar 11, 2009, at 10:43 PM, chris.ne...@utoronto.ca wrote: I was either using using 3.3 or 3.3.1, certainly not 3.1.4 or 3.2.1. It looks like the change was in 3.3.1, possibly by Erik:

Re: [gmx-users] get a box of 100 molecules

Adrien Delmont wrote: The molecule I use is a simple hydrocarbon ( n-heptane ) and I think that I should add something like dihedral, bond, angle parameters after I search the literature. I found some information about that. I think I will add parameters into the related force fields .itp fi

Re: [gmx-users] get a box of 100 molecules

--- On Wed, 3/11/09, Adrien Delmont wrote: From: Adrien Delmont Subject: Re: [gmx-users] get a box of 100 molecules To: jalem...@vt.edu Date: Wednesday, March 11, 2009, 9:46 PM The molecule I use is a simple hydrocarbon ( n-heptane ) and I think that I should add something like  dihedr

[gmx-users] phi / psi values using g_chi

I was either using using 3.3 or 3.3.1, certainly not 3.1.4 or 3.2.1. It looks like the change was in 3.3.1, possibly by Erik: [tera:~]?diff gromacs-3.3/src/tools/gmx_chi.c gromacs-3.3.1/src/tools/gmx_chi.c 2c2 < * $Id: gmx_chi.c,v 1.3 2005/02/16 17:39:27 hess Exp $ --- * $Id: gmx_chi.c,v 1

Re: [gmx-users] get a box of 100 molecules

Adrien Delmont wrote: I just want to add missing parameters for my molecule in order to get ..gro and top files for example GROMOS96 43a2 force field . How can I add missing parameters ? I didn't find any information about this procedure. I'm waiting for your help. You'll have to define

Re: [gmx-users] get a box of 100 molecules

  I just want to add missing parameters for my molecule in order to get .gro and top files for example GROMOS96 43a2 force field . How can I add missing parameters ? I didn't find any information about this procedure. I'm waiting for your help.   Thanks in advance --- On Wed, 3/11/09, Mark Abr

Re: [gmx-users] redirect md.log to standard ourput

ok thanks, if it becomes critical to troubleshooting, I'll just get my hands dirty with the cpp code. On Wed, Mar 11, 2009 at 1:01 PM, Mark Abraham wrote: > Jack Shultz wrote: > >> I'm trying to capture errors when I run simulations through boinc. Is >> there a way to redirect the log to the stan

Re: [gmx-users] Broken trr-file

Justin A. Lemkul wrote: Hansjoerg Jerabek wrote: Dear Mark! At first: thanks for your reply. The log file has been witten correctly, and gmxcheck gives me the following warning: Checking file ketamine.t2.trr trn version: GMX_trn_file (double precision) Reading frame 0 time

Re: [gmx-users] problems with gmxtest.pl

Bernhard Bandow wrote: Dear users and developers of gromacs, following the installation of gromacs 4.0.3 the tests show some inconsistencies. The software was compiled with Intel 11.0.069 compiler using mvapich2 Further options in configure were: --enable-fortran --enable-mpi --with-fft=mkl --en

Re: [gmx-users] problems with gmxtest.pl

Bernhard Bandow wrote: Dear users and developers of gromacs, following the installation of gromacs 4.0.3 the tests show some inconsistencies. The software was compiled with Intel 11.0.069 compiler using mvapich2 Further options in configure were: --enable-fortran --enable-mpi --with-fft=mkl --

Re: [gmx-users] problems with gmxtest.pl

Bernhard Bandow wrote: Dear users and developers of gromacs, following the installation of gromacs 4.0.3 the tests show some inconsistencies. The software was compiled with Intel 11.0.069 compiler using mvapich2 Further options in configure were: --enable-fortran --enable-mpi --with-fft=mkl --en

Re: [gmx-users] problem about compiling mdrun_mpi under cygwin

Xiang Mao wrote: Hi, there: I met a problem when I try to compile mdrun_mpi using configure --enable-mpi, I have mpich2 installed. I got some error message like the following(sorry, it is too long, hope you do not mind). I am wondering if anyone could tell me how to deal with it. Thank yo

Re: [gmx-users] phi / psi values using g_chi

Hi Chris, Thanks for the link. I then do not understand what is happening because I get the same exact values with g_chi and g_rama! Are you sure you were using the gmx-3.3.1? And not an earlier version? Note that in the code of gmx-3.1.4 and gmx-3.2.1 the non-standard definition is use

Re: [gmx-users] RE : big system

noob noob wrote: Dear all, If I have available computing resources and hard disk space..i have no worries already...right? How about the parameters? because I performed the smaller system (smae types of molecules) and now I wanna perform a bigger system with increasing the number of mole

Re: [gmx-users] redirect md.log to standard ourput

Jack Shultz wrote: I'm trying to capture errors when I run simulations through boinc. Is there a way to redirect the log to the standard output? Not with the existing implementation. The result would be a confusing mess of the existing stdout and the .log file, anyway. Mark _

[gmx-users] problems with gmxtest.pl

Dear users and developers of gromacs, following the installation of gromacs 4.0.3 the tests show some inconsistencies. The software was compiled with Intel 11.0.069 compiler using mvapich2 Further options in configure were: --enable-fortran --enable-mpi --with-fft=mkl --enable-shared The system gr

Re: [gmx-users] get a box of 100 molecules

Adrien Delmont wrote: *From:* Adrien Delmont *To:* jalem...@vt.edu *Sent:* Wednesday, March 11, 2009 6:09:53 PM *Subject:* Re: [gmx-users] get a box of 100 molecules I didn't get gro and top files with any force field in

[gmx-users] RE : big system

Dear all, If I have available computing resources and hard disk space..i have no worries already...right? How about the parameters? because I performed the smaller system (smae types of molecules) and now I wanna perform a bigger system with increasing the number of molecules and box

[gmx-users] problem about compiling mdrun_mpi under cygwin

Hi, there: I met a problem when I try to compile mdrun_mpi using configure --enable-mpi, I have mpich2 installed. I got some error message like the following(sorry, it is too long, hope you do not mind). I am wondering if anyone could tell me how to deal with it. Thank you so much. Best wishe

Re: [gmx-users] get a box of 100 molecules

From: Adrien Delmont To: jalem...@vt.edu Sent: Wednesday, March 11, 2009 6:09:53 PM Subject: Re: [gmx-users] get a box of 100 molecules I didn't get gro and top files with any force field in Gromacs. I basicly want to use oplsaa and GROMOS96 43a2 force fiel

Re: [gmx-users] initial velocities Langevin dynamics

Hi Loris, It may be better to have ld_seed=-1. This way, you won't have the same seed again when you restart. @Article{Cerutti2008, author = "Cerutti, D S and Duke, R and Freddolino, P L and Fan, H and Lybrand, T P", title = {Vulnerability in Popular Molecular Dynamics Packages Concerning Langevi

[gmx-users] phi / psi values using g_chi

two questions relative to g_chi from the gmx-3.3.1 but gmx-4.0.2 uses similar code. 1) In the header of g_chi obtained using the -h option there is a "bug" that indicates that the phi/psi angles are not calculated as the usual C(-)-N-CA-C and N- CA-C-N(+) definitions but H-N-CA-C and N-CA-C-

Re: [gmx-users] get a box of 100 molecules

Adrien Delmont wrote: /Dear Users, I'm new to Gromacs. Before I try to generate a box of 100 molecules, I wanted to ask it to the users. Can I get a box of 100 molecules that are randomly //distributed/ /and not attached to each other using the commands below? If there are something wrong in

Re: [gmx-users] big system

noob noob wrote: Dear all, I have some Questions here, what are the things or factors that we need to consider when we wanna perform big system simulation?(eg: volume of 5000 nm3 o 8000 nm3) Whether or not you have available computing resources and hard disk space. -Justin Thanks for

[gmx-users] redirect md.log to standard ourput

I'm trying to capture errors when I run simulations through boinc. Is there a way to redirect the log to the standard output? -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx

[gmx-users] get a box of 100 molecules

Dear Users, I'm new to Gromacs. Before I try to generate a box of 100 molecules, I wanted to ask it to the users. Can I get a box of 100 molecules that are randomly distributed and not attached to each other using the commands below? If there are something wrong in commands please share your v

[gmx-users] big system

Dear all, I have some Questions here, what are the things or factors that we need to consider when we wanna perform big system simulation?(eg: volume of 5000 nm3 o 8000 nm3) Thanks for any comments. _ More than messages–

Re: [gmx-users] initial velocities Langevin dynamics

Dear Mark and Oscar, Thanks for your help! I checked the velocity distribution and the velocity at different simulation frames. As you said the initial velocities are all set to zero and at the next step are already changed, I also guess by the random thermal noise. Thus, my idea of simulating

Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?

Omer Markovitch wrote: Use: trjconv -f conf.gro -s conf.gro -o conf.pdb. Note the use of "-s" on the same gro file. or editconf -h --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/

Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?

Use: trjconv -f conf.gro -s conf.gro -o conf.pdb. Note the use of "-s" on the same gro file. --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] initial velocities Langevin dynamics

> > Thus I am a bit confused about it! >> > > I'm confused about the manual comment about only being meaningful with the > MD integrator, but we'll have to wait until someone who knows something > about LD can post! For LD, the velocities will (should) get rescaled by the random thermal noise, th

Re: [gmx-users] Broken trr-file

Hansjoerg Jerabek wrote: Dear Mark! At first: thanks for your reply. The log file has been witten correctly, and gmxcheck gives me the following warning: Checking file ketamine.t2.trr trn version: GMX_trn_file (double precision) Reading frame 0 time 43500.000 # Atoms 25

Re: [gmx-users] Broken trr-file

Dear Mark! At first: thanks for your reply. The log file has been witten correctly, and gmxcheck gives me the following warning: Checking file ketamine.t2.trr trn version: GMX_trn_file (double precision) Reading frame 0 time 43500.000 # Atoms 25400 Reading frame

[gmx-users] phi / psi values using g_chi

Dears, two questions relative to g_chi from the gmx-3.3.1 but gmx-4.0.2 uses similar code. 1) In the header of g_chi obtained using the -h option there is a "bug" that indicates that the phi/psi angles are not calculated as the usual C(-)-N-CA-C and N- CA-C-N(+) definitions but H-N-CA-C

Re: [gmx-users] Broken trr-file

Hansjoerg Jerabek wrote: Dear colleagues! I faced a problem while trying to modify a trr-file using trjconv_d: trjconv_d -f ketamine.t2.trr -s ketamine.2.tpr -n bilayer.ndx -o ketamine.2.trr -b 43550 In my case the first frame of the trr-file starts at 43500ps (time step: 5ps). I get t

Re: [gmx-users] initial velocities Langevin dynamics

Loris Moretti wrote: Dear Mark, Thanks for answering! My question arises because in the manual is also reported that gen_vel "is only meaningful with integrator md" (mdp options section: velocity generation) Well it is much more effective to say that the first time. :-) Getting someone's att

[gmx-users] Broken trr-file

Dear colleagues! I faced a problem while trying to modify a trr-file using trjconv_d: trjconv_d -f ketamine.t2.trr -s ketamine.2.tpr -n bilayer.ndx -o ketamine.2.trr -b 43550 In my case the first frame of the trr-file starts at 43500ps (time step: 5ps). I get the following ouput: Wi

Re: [gmx-users] initial velocities Langevin dynamics

Dear Mark, Thanks for answering! My question arises because in the manual is also reported that gen_vel "is only meaningful with integrator md" (mdp options section: velocity generation) and because I provide a .gro file with no velocities and I clearly specify in the .mdp not to generate veloc

Re: [gmx-users] initial velocities Langevin dynamics

Loris Moretti wrote: Hello everybody, Sorry to post again the same question but I've got no answer so far. I have a technical question, it might be silly but I couldn't find an answer so far. How are assigned the initial velocities for the particles when Langevin dynamics is performed? In no

[gmx-users] initial velocities Langevin dynamics

Hello everybody, Sorry to post again the same question but I've got no answer so far. I have a technical question, it might be silly but I couldn't find an answer so far. How are assigned the initial velocities for the particles when Langevin dynamics is performed? In normal MD the gen_vel/gen

Re: [gmx-users] metal ion go out of protein after md

Nothing, except reading more about periodic boundary conditions. It doesn't hurt though to understand that binding of ions such as Mn to proteins involves charge transfer effects, that are hard to model properly. This will cause a (further) deviation between your results and reality. So be careful

Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?

Andrew Voronkov wrote: Dear GROMACS users, is there a possibility to convert .gro files directly to PDB? Or I can do it only with .tpr? I've tried gro2pdb -f conf.gro -o conf.pdb but it doesn't work. I've never heard of it, so that utility probably doesn't exist! There's a section in the GROM

Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?

Hi Andrew, I would do it with editconf with the same options. Regards Andrea 2009/3/11 Andrew Voronkov : > Dear GROMACS users, > is there a possibility to convert .gro files directly to PDB? Or I can do it > only with .tpr? > I've tried gro2pdb -f conf.gro -o conf.pdb > but it doesn't work. >

[gmx-users] is there a possibility to convert .gro files directly to PDB?

Dear GROMACS users, is there a possibility to convert .gro files directly to PDB? Or I can do it only with .tpr? I've tried gro2pdb -f conf.gro -o conf.pdb but it doesn't work. Best regards, Andrew ___ gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] metal ion go out of protein after md

Hi MN in my active site participate in electrostatic intraction. I did not define any covalant bonds in topology file. What should I do in the case of Electrostatic intraction? -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous c

RE: [gmx-users] metal ion go out of protein after md

Hi, How is your metal ions bound to the active site? Did you make explicit covalent bonds for them in your topology file? Best regards, Tri -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Homa Azizian Sent: Wed 3/11/2009 2:59 PM To: gmx-users@gromacs.org Subject: [

Re: [gmx-users] how could have integrated structure after sa.

Homa Azizian wrote: Hi 1- Is it possible to change the pbc condition from xyz(default) to no(vacume) after finishing the annealing, in order to reach an integrated sturcture instead of wraped one? 2- What command should I execute? is fixed by trjconv? 3-It is probably a simple question, in M

[gmx-users] metal ion go out of protein after md

Hi after 30 ns MD, the 2 metal ion (MN) jumpe out of their active site, why does it ocure? how could I fix this problem, is it necessary to do the job again? Thank's for replying. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerou

[gmx-users] how could have integrated structure after sa.

Hi 1- Is it possible to change the pbc condition from xyz(default) to no(vacume) after finishing the annealing, in order to reach an integrated sturcture instead of wraped one? 2- What command should I execute? is fixed by trjconv? 3-It is probably a simple question, in MD we have also PBC set