[gmx-users] Help with g_rmsf
Hi everyone, please I have a litle problem: during my simulation, the dimer I'm simulating changed a lot. So when I calculate with g_rms, the RMSD between my initial and my final structure (choosing Protein-H), I get a value of 10 angstroms. However, when I try to calculate a RMSDeviation averaged over residue using g_rmsf -od , between the first chain of the initial and final structure, I get RMSDeviation per residue values that don't exceed 3 or 4 angstroms. Please can anyone explain how g_rmsf works? If I do the following: g_rmsf -s initial.pdb -f final.pdb -od rmsdev.xvg -res (I choose chainA-H), does g_rmsf fit one the whole dimer and then calculate rmsdeviation of chainA or does it fit on chainA and then calculate RMSdeviation of chainA. In the latter case, my result does not reflect the reality of my simulation. Please if anyone knows the answer, I would really appreciate some help. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] vdwtype = cut-off
Hi everyone, I ran my simulations with these parameters: nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 vdwtype = cut-off rvdw= 1.2 Apparently, in Gromacs, when using vdwtype = cut-off, the potential changes discontinuously. However, I have a constant LJ(SR) energy and a constant LJ(LR) energy, although I didn't use either Switch or Shift. Please can anyone explain how does the cut-off really works in Gromacs and whether my simulations are correct or not? 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_tune_pme
Hi everyone, please I was running simulations with gromacs version 4.0.3
,but I got the following error:
Average load imbalance: 12.1 %
Part of the total run time spent waiting due to load imbalance: 6.9 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0
% Y 9 %
Average PME mesh/force load: 0.807
Part of the total run time spent waiting due to PP/PME imbalance: 5.3 %
NOTE: 6.9 % performance was lost due to load imbalance
in the domain decomposition.
NOTE: 5.3 % performance was lost because the PME nodes
had less work to do than the PP nodes.
You might want to decrease the number of PME nodes
or decrease the cut-off and the grid spacing.
After searching the archive mailing list and reading the manual , I decided
to use g_tune_pme so I switched to gromacs 4.5.4. Here's my script:
#PBS -S /bin/bash
#PBS -N job_md6ns
#PBS -e job_md6ns.err
#PBS -o job_md6ns.log
#PBS -m ae -M carlajam...@gmail.com
#PBS -l select=2:ncpus=8:mpiprocs=8
#PBS -l walltime=024:00:00
cd $PBS_O_WORKDIR
export GMXLIB=$GMXLIB:/scratch/carla/top:.
module load gromacs
chem=/opt/software/SGI/gromacs/4.5.4/bin/
mdrunmpi=mpiexec /opt/software/SGI/gromacs/4.5.4/bin/
${chem}grompp -v -f md6ns.mdp -c 1rlu_apo_mdeq.gro -o 1rlu_apo_md6ns.tpr -p
1rlu_apo.top
${mdrunmpi}g_tune_pme -v -s 1rlu_apo_md6ns.tpr -o 1rlu_apo_md6ns.trr -cpo
state_6ns.cpt -c 1rlu_apo_md6ns.gro -x 1rlu_apo_md6ns.xtc -e md6ns.edr -g
md6ns.log -np 4 -ntpr 1 -launch
But now, I have the following error message:
Fatal error:
Library file residuetypes.dat not found in current dir nor in your GMXLIB
path.
Except that I'm using amber94 force-field and that my topology files are in
a special directory called top where I modified certain things. With gromacs
4.0.3, it always worked so I don't know what is happening here.
Please does anyone have an idea of what it might be?
Do I have to run pdb2gmx, editconf, etc... with the gromacs 4.5.4 for it to
work?
Thank you,
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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Fatal error: file type out of range (48)
Hi,
Please does anyone Know what this error means?
Fatal error:
file type out of range (48)
Here's my script:
#PBS -S /bin/bash
#PBS -N job_md6ns
#PBS -e job_md6ns.err
#PBS -o job_md6ns.log
#PBS -m ae -M carlajam...@gmail.com
#PBS -l select=2:ncpus=8:mpiprocs=8
#PBS -l walltime=024:00:00
cd $PBS_O_WORKDIR
export GMXLIB=$GMXLIB:/scratch/carla/top:.
module load gromacs
mdrunmpi=mpiexec /opt/software/SGI/gromacs/4.5.4/bin/mdrun
${mdrunmpi} -v -s .tpr -o .trr -cpo state_6ns.cpt -c .gro -x .xtc -e
.edr -g .log
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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Residence time and trjorder
Hi Baofu, Please can you tell me how to install g_residence.c in gromacs? If I understood well, the line command is the following: g_residence -s toplogy.tpr -f trajectory.xtc -o output What is the format of the output? Thank you, Carla On Tue, Jul 12, 2011 at 2:32 PM, Baofu Qiao qia...@gmail.com wrote: HI Carla, I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly. regards, Baofu Qiao On 07/12/2011 02:04 PM, Carla Jamous wrote: Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my protein. trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 But now I need to analyse the residence time of a water molecule, I mean the number of times a single water molecule stays in a radius of 5 A of the protein and divide this number by the total number of conformations, in order to have a pourcentage value. Please is there any gromacs tool able to do this calculation or else does anyone have an idea of how to do that? Thank you 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Residence time and trjorder
Dear Xavier, my problem is the following: I'm trying to figure out if a water molecule is present in a specific area around my protein and if so, which water molecule is that and how long does it stay in that place. As you said, if I google residence time, here's the definition: *Residence time* (also known as *removal time*) is the average amount of time that a particle http://en.wikipedia.org/wiki/Particle spends in a particular system. But I don't find a tool to calculate this residence time in gromacs, so I'm trying to find a trick that can give me a pourcentage of the time of my simulation where a certain water molecule stays in the specific area of my protein. Regards, Carla On Tue, Jul 12, 2011 at 5:51 PM, XAvier Periole x.peri...@rug.nl wrote: Dear Boafu, This sounds like a great tool! Carla, note that once you've ordered the water molecules you loose the continuity of their trajectories ... that is because you order them in function of their distance to the protein. I am not sure the definition you give will give you the answer to the residence time. you can google residence time and proteins and see what come out :)) XAvier. On Jul 12, 2011, at 6:32 AM, Baofu Qiao wrote: HI Carla, I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly. regards, Baofu Qiao On 07/12/2011 02:04 PM, Carla Jamous wrote: Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my protein. trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 But now I need to analyse the residence time of a water molecule, I mean the number of times a single water molecule stays in a radius of 5 A of the protein and divide this number by the total number of conformations, in order to have a pourcentage value. Please is there any gromacs tool able to do this calculation or else does anyone have an idea of how to do that? Thank you Carla g_residence.c-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Residence time and trjorder
Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my protein. trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 But now I need to analyse the residence time of a water molecule, I mean the number of times a single water molecule stays in a radius of 5 A of the protein and divide this number by the total number of conformations, in order to have a pourcentage value. Please is there any gromacs tool able to do this calculation or else does anyone have an idea of how to do that? Thank you 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Problem with g_rdf plot
Hi everyone, I ran a water simulation and I tried to calculate radial distribution function OO but I get strange peaks from r =1.5nm onwards. I have 8 atoms in a box of 9.5. I post the graph as an attached file. Please does anyone have an idea of what might be going on? Thanks, Carla rdf_Ow-Ow-15to17ns.dat Description: MOPAC data rdf_Ow-Ow-15to17ns.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] PBC
Hi everyone, In my .mdp MD file, I didn't put pbc =xyz. Then, I used tpbconv and mdrun to continue my simulation. My question is: did I run my simulation using periodic boundary conditions because I have the impression that I did but I'm not sure if not using the mention pbc in my mdp file means that I didn't use PBC? 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PBC
Thank you Justin, indeed it's pbc = xyz in my md.log file. Carla On Fri, Feb 25, 2011 at 3:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, In my .mdp MD file, I didn't put pbc =xyz. Then, I used tpbconv and mdrun to continue my simulation. My question is: did I run my simulation using periodic boundary conditions because I have the impression that I did but I'm not sure if not using the mention pbc in my mdp file means that I didn't use PBC? pbc=xyz is the default if not specified. Check your mdout.mdp and md.log files to be sure. -Justin Thanks Carla -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Minimisation restraints
Hi everyone, please I don't have access to the mailing list, (there must be a problem in the archive) and I need to know if there's a way of doing energy minimisation with restraints on the backbone. In other words, I want to minimize the sidechaines in my protein without moving (or minimizing) the backbone. Please has anyone done this before? Thank you. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet
Thank you, It worked, one last question. Something is not very clear to me: -ov: plots the average angle of a group of angles as a function of time!! What does it mean? Because I'm getting positive and negative values in the same plot. Are these values the values of my dihedral angle as a function of time? Thanks again, Carla On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey kgp.a...@gmail.com wrote: try the -type option with dihedral amit On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous carlajam...@gmail.comwrote: Hi Everyone, Please I'm trying to calculate one dihedral angle as a function of time during my simulation. For this, I used g_angle. In the manual (version 4.0.3) it says: the indexfile should contain atom-triplets or atom-quadruplets for dihedrals. I put an atom-quadruplet in my index file, but when I run g_angle -f .xtc -n .ndx -od .xvg and I select the group of atom-quadruplets, gromacs crashes and shows this error message: number of index elements not multiple of 3, these can not be angle triplets So actually g_angle only calculates angles not dihedrals? 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_principal
Hi everyone, I'm trying to use g_principal for the first time. It gives 4 output files: axis1, axis2, axis3 moi.dat My question is: how can I know which axis correponds to the lowest eigenvalue? Nothing is mentioned in the manual. Thank you. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] perl script for g_hbond
Hi, you should probably do: perl HB.pl -s .pdb -map .xpm -index .xpm More details are written inside the perl script. Cheers, Carla On Tue, Nov 23, 2010 at 4:32 PM, leila karami karami.lei...@gmail.comwrote: Dear Justin I study simulation of pr-dna complex. I want to know the percentage of existence of each hbond during my trajectory. I searched in previous lists. I want to use Perl script you offered to carla jamous: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054727.html I'm biginner in using of Perl script, when I use your Perl script, Execution of ./HB.pl aborted due to compilation errors. how to fix it? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_sas and g_rdf
Hi everyone, I'm trying to look at the radial distribution function of water around the surface of my protein. For that, I calculated the surface area per residue (g_sas -or). Since I didn't find in the litterature any criteria to choose a minimum area value to count a residue as a a surface residue, I chose to analyze the residues that have an area value 1.3 nm2 I counted 23 residues that have area values 1.3 nm2 I made an index file with one index group for each residue and on index group for SOL_OW Then I ran g_rdf on my trajectory g_rdf -s .tpr -f .xtc -n .ndx -o rdf.xvg -bin 0.02 -com I chose: reference group=the residue I want to analyze group = SOL_OW even though I'm analyzing the residues that have large surface area values, my RDF plot doesn't look like what I was execting: it means an RDF plot with a peak at g(r)=2 or 3 then a decrease in g(r) and finally a g(r)=1 My peak is at g(r)=0.7 and then it increases to g(r)=1 Does anyone have an idea why I have this kind of plot? Because I didn't find any answers in the mailing list. Thank you, 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
Hi everyone, I ran g_hbond on a trajectory. When g_hbond asks for two groups in the index file, I give: group1: Protein group2: ligand The output .ndx file contains 44 Hbonds. In order to verify my result on each and every Hbond, I ran g_hbond on the same trajectory but this time in my index file, I gave atom triplets, so when g_hbond asks for two groups, I give for example: group1: a4810_a4811_a1857 group2: a4810_a4811_a1857 Surprisingly, 10 of the 44 Hbonds are not found using this method. Am I doing something wrong or is there a problem with g_hbond? Thank you, 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_sas resarea.xvg
Hi everyone, I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg What I don't understand is why there are 3 columns in the file resarea.xvg although this is what's written in my file: # g_sas is part of G R O M A C S: # # GROtesk MACabre and Sinister # @title Area per residue @xaxis label Residue @yaxis label Area (nm\S2\N) @TYPE xy So I would expect this file to contain only two columns. I'm using gromacs version 4.0.3. Thanks for your help, 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_hbond
Hi Erik, I tried what you said: I made index groups containing only the atoms involved in that hbond and ran g_hbond again. The problem didn't persist. So I wanted to check if I misinterpreted the map: for that, I compared my 4 index files: the one of my concatenated trajectory and the three of the separate trajectories. When I look at this comparison table and then at my concatenated hbond map, the results don't match: for example, the Hbond that has the number 1 in my concatenated trajectory doesn't appear in my concatenated map (it means that in my map, next to y=1, nothing appears), however, this same H-bond (same number of atoms involved) exists in my first and my third trajectories' index files. So please could you explain how to interpret the map and if next to some y value in my map, nothing appears, is this value taken into account in my index file? Thank you, Carla On Tue, Nov 2, 2010 at 8:36 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Erik Marklund skrev 2010-11-02 20.33: Carla Jamous skrev 2010-11-02 17.35: Hi to all, I'm sorry I'm asking again a question I asked a week ago but I still haven't found my answer: I concatenated 3 trajectories of 3 different molecules (that have the same number of atoms) with trjcat: trjcat -settime Then I ran g_hbond on the concatenated trajectory, I got an index.ndx file that contains an H-bond between the Thr121 of my protein and an atom N2 of my ligand. This H_bond figures in the 3 trajectories when I look at the hbmap of my concatenated trajectory. On the other hand, I ran g_hbond on each of the 3 different trajectories. This H_bond doesn't exist in the index files of two of my trajectories. So it doesn't match the result I get with my concatenated trajectory. To be sure that this result is right, I calculated the angle and the r of my H-bond in VMD during each of the 3 trajectories and the results indicate that this H-bond doesn't exist (I consider that r must be or equal to 0.35 nm and angle or equal to 30 degrees). Please can anyone tell me why the results of g_hbond in my concatenated trajectory don't match the results of g_hbond on each of my trajectories? Thank you Carla Hi, This sounds strange. Could you file a bugzilla and either upload the trajectories+tpr, or, if the files are huge, make them available my other means? I need to have a closer look, perhaps through a debugger. A simple test you could do yourself is to make index groups containing only the atoms involved in that hbond and run g_hbond again. If the problem persists, then it looks like a bug. If not, then I still can't rule out misinterpretation of the matrix. Erik -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_hbond
Hi to all, I'm sorry I'm asking again a question I asked a week ago but I still haven't found my answer: I concatenated 3 trajectories of 3 different molecules (that have the same number of atoms) with trjcat: trjcat -settime Then I ran g_hbond on the concatenated trajectory, I got an index.ndx file that contains an H-bond between the Thr121 of my protein and an atom N2 of my ligand. This H_bond figures in the 3 trajectories when I look at the hbmap of my concatenated trajectory. On the other hand, I ran g_hbond on each of the 3 different trajectories. This H_bond doesn't exist in the index files of two of my trajectories. So it doesn't match the result I get with my concatenated trajectory. To be sure that this result is right, I calculated the angle and the r of my H-bond in VMD during each of the 3 trajectories and the results indicate that this H-bond doesn't exist (I consider that r must be or equal to 0.35 nm and angle or equal to 30 degrees). Please can anyone tell me why the results of g_hbond in my concatenated trajectory don't match the results of g_hbond on each of my trajectories? Thank you 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Electrostatic interactions between residues
Hi everyone, please is there a way to know if electrostatic interactions exist between my ligand and my protein during the trajectory? Which tool can I use for this purpose, other than g_saltbr? Thank you, 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Percentage of H-bonds
; $o++) {
printf(OUT %10s\t%10s\t%10s\t%10s\t%10.3f\n, $donor_resn[$o],
$donor_names[$o], $acceptor_resn[$o], $acceptor_names[$o],
(($hbonds{$o}/$nframes)*100));
}
close(OUT);
exit;
Carla Jamous wrote:
Hi everyone,
I tried to analyze the H-bonds in my trajectory with g-hbond and I
analysed the xpm and ndx file. But now I need to know the percentage of
existence of each hbond during my trajectory. Is there a way to do it with a
command line? Or is there a program (someone told me there are python
programs for analysis of gromacs trajectories) to extract this information
from the .xpm file?
Thank you.
Cheers,
Carla
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Percentage of H-bonds
Please I have a problem:
I concatenated 3 trajectories and got one long trajectory on which I ran the
perl script it gives me lets say 60% for hbond 1.
But when I look in each of the 3 trajectories alone, this hbond doesn't even
exist in 2 of them.
Do you have an idea where the problem might be because I checked if it's
well concatenated and it is. And I can't figure out why I have this error.
Thanks,
Carla
On Tue, Oct 26, 2010 at 2:08 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Carla Jamous wrote:
Hi Justin,
Please can you explain this particular comment in your perl script: #
There should now be $nres lines left in the file
# The HB map for the last index is written first (top-down in .xpm file)
# * Element 0 is index $nres, element 1 is $nres-1, etc.
Is the perl script reading the index file beginning from the bottom? If
so, why is that? Because in the manual, it says that in the matrix, the
ordering is identical to that in the index file.
The order is the same, and the indices are mapped exactly as you would
expect them. The .xpm file is written, however, from top down. So the
final index in hbond.ndx is the top line in the matrix. As such, even
though they are in the same order, per se, the two files (.xpm and .ndx)
have to be read in opposite directions.
-Justin
Thank you.
Carla
On Mon, Oct 11, 2010 at 4:31 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
I wrote a Perl script to do a similar task (appended below).
Perhaps it will be useful to you. I hope it works; I had to hack
out some things that were specific to my needs and have done only
limited testing.
-Justin
#!/usr/bin/perl
#
# plot_hbmap.pl http://plot_hbmap.pl - plot the probability of
finding a particular hydrogen bond
# based on several input files:
# 1. coordinate file (for atom naming) - MUST be a .pdb file with
NO CHAIN IDENTIFIERS
# 2. hbmap.xpm
# 3. hbond.ndx (modified to contain only the atom numbers in the
[hbonds...] section, nothing else)
#
use strict;
unless(@ARGV) {
die Usage: perl $0 -s structure.pdb -map hbmap.xpm -index
hbond.ndx\n;
}
# define input hash
my %args = @ARGV;
# input variables
my $map_in;
my $struct;
my $ndx;
if (exists($args{-map})) {
$map_in = $args{-map};
} else {
die No -map specified!\n;
}
if (exists($args{-s})) {
$struct = $args{-s};
} else {
die No -s specified!\n;
}
if (exists($args{-index})) {
$ndx = $args{-index};
} else {
die No -index specified!\n;
}
# open the input
open(MAP, $map_in) || die Cannot open input map file!\n;
my @map = MAP;
close(MAP);
open(STRUCT, $struct) || die Cannot open input coordinate file!\n;
my @coord = STRUCT;
close(STRUCT);
open(NDX, $ndx) || die Cannot open input index file!\n;
my @index = NDX;
close(NDX);
# determine number of HB indices and frames
my $nres = 0;
my $nframes = 0;
for (my $i=0; $iscalar(@map); $i++) {
if ($map[$i] =~ /static char/) {
my $res_line = $map[$i+1];
my @info = split( , $res_line);
$nframes = $info[0];
my @nframes = split('', $nframes);
shift(@nframes);# get rid of the
$nframes = join('', @nframes);
$nres = $info[1];
}
}
print Processing the map file...\n;
print There are $nres HB indices.\n;
print There are $nframes frames.\n;
# initialize hashes for later output writing
# counter $a holds the HB index from hbond.ndx
my %hbonds;
for (my $a=0; $a$nres; $a++) {
$hbonds{$a+1} = 0;
}
# donor/acceptor hashes for bookkeeping purposes
my %donors;
for (my $b=1; $b=$nres; $b++) {
$donors{$b} = 0;
}
my %acceptors;
for (my $c=1; $c=$nres; $c++) {
$acceptors{$c} = 0;
}
# clean up the output - up to 18 lines of comments, etc.
splice(@map, 0, 18);
# remove any x-axis or y-axis lines
for (my $n=0; $nscalar(@map); $n++) {
if (($map[$n] =~ /x-axis/) || ($map[$n] =~ /y-axis/)) {
shift(@map);
$n--;
}
}
# There should now be $nres lines left in the file
# The HB map for the last index is written first (top-down in .xpm
file)
# * Element 0 is index $nres, element 1 is $nres-1, etc.
for (my $i=$nres; $i=1; $i--) {
# There will be $nframes+2 elements in @line (extra two are at
beginning
# and end of the line)
# Establish a conversion factor and split the input lines
my $j = $nres - $i;
my @line = split('', $map[$j]);
# for each index, write to hash
for (my $k=1; $k=($nframes+1); $k++) {
if ($line[$k] =~ /o/) {
$hbonds{$i}++;
}
}
}
print Processing the index file...\n
Re: [gmx-users] Percentage of H-bonds
Yes, I'm always looking at the same one, it means the corresponding one in
the other trajectory.
Carla
On Tue, Oct 26, 2010 at 2:17 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Carla Jamous wrote:
Please I have a problem:
I concatenated 3 trajectories and got one long trajectory on which I ran
the perl script it gives me lets say 60% for hbond 1.
But when I look in each of the 3 trajectories alone, this hbond doesn't
even exist in 2 of them.
Do you have an idea where the problem might be because I checked if it's
well concatenated and it is. And I can't figure out why I have this error.
The hydrogen bond indices are regenerated in each trajectory, since not all
H-bonds might be present in the same order. Are you sure you're continually
looking at the same one?
-Justin
Thanks,
Carla
On Tue, Oct 26, 2010 at 2:08 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Carla Jamous wrote:
Hi Justin,
Please can you explain this particular comment in your perl
script: # There should now be $nres lines left in the file
# The HB map for the last index is written first (top-down in
.xpm file)
# * Element 0 is index $nres, element 1 is $nres-1, etc.
Is the perl script reading the index file beginning from the
bottom? If so, why is that? Because in the manual, it says that
in the matrix, the ordering is identical to that in the index file.
The order is the same, and the indices are mapped exactly as you
would expect them. The .xpm file is written, however, from top
down. So the final index in hbond.ndx is the top line in the
matrix. As such, even though they are in the same order, per se,
the two files (.xpm and .ndx) have to be read in opposite directions.
-Justin
Thank you.
Carla
On Mon, Oct 11, 2010 at 4:31 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:
I wrote a Perl script to do a similar task (appended below).
Perhaps it will be useful to you. I hope it works; I had to
hack
out some things that were specific to my needs and have done
only
limited testing.
-Justin
#!/usr/bin/perl
#
# plot_hbmap.pl http://plot_hbmap.pl http://plot_hbmap.pl
- plot the probability of
finding a particular hydrogen bond
# based on several input files:
# 1. coordinate file (for atom naming) - MUST be a .pdb
file with
NO CHAIN IDENTIFIERS
# 2. hbmap.xpm
# 3. hbond.ndx (modified to contain only the atom numbers
in the
[hbonds...] section, nothing else)
#
use strict;
unless(@ARGV) {
die Usage: perl $0 -s structure.pdb -map hbmap.xpm -index
hbond.ndx\n;
}
# define input hash
my %args = @ARGV;
# input variables
my $map_in;
my $struct;
my $ndx;
if (exists($args{-map})) {
$map_in = $args{-map};
} else {
die No -map specified!\n;
}
if (exists($args{-s})) {
$struct = $args{-s};
} else {
die No -s specified!\n;
}
if (exists($args{-index})) {
$ndx = $args{-index};
} else {
die No -index specified!\n;
}
# open the input
open(MAP, $map_in) || die Cannot open input map file!\n;
my @map = MAP;
close(MAP);
open(STRUCT, $struct) || die Cannot open input coordinate
file!\n;
my @coord = STRUCT;
close(STRUCT);
open(NDX, $ndx) || die Cannot open input index file!\n;
my @index = NDX;
close(NDX);
# determine number of HB indices and frames
my $nres = 0;
my $nframes = 0;
for (my $i=0; $iscalar(@map); $i++) {
if ($map[$i] =~ /static char/) {
my $res_line = $map[$i+1];
my @info = split( , $res_line);
$nframes = $info[0];
my @nframes = split('', $nframes);
shift(@nframes);# get rid of the
$nframes = join('', @nframes);
$nres = $info[1];
}
}
print Processing the map file...\n;
print There are $nres HB indices.\n;
print There are $nframes frames.\n;
# initialize hashes for later output writing
# counter $a holds the HB index from hbond.ndx
my %hbonds;
for (my $a=0; $a$nres; $a++) {
$hbonds{$a+1} = 0;
}
# donor/acceptor hashes
[gmx-users] g_hbond on concatenated trajectory
Hi everyone, please I need some help on g_hbond. I concatenated 3 trajectories. I ran g_hbond on the concatenated trajectory. I got the result of h_bonds. Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a different result, it means: if I take the first 10ps of my concatenated trajectory and I run g_hbond on these 10ps. I get some H-bonds eg. Gly(N)...H(gly)...O but this same H-bond doesn't appear in the first 10ps of my concatenated trajectory's HBmap. Please does anyone have an idea where I might have done a mistake? Thank you, 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_hbond on concatenated trajectory
No, I don't think so because I did an .eps file (with xpm2ps) that indicates the Time(ps) in x-axis and Hydrogen Bond Index in y-axis. This is the way I'm reading my matrix. Carla On Fri, Oct 15, 2010 at 12:09 PM, Erik Marklund er...@xray.bmc.uu.sewrote: Carla Jamous skrev 2010-10-15 12.05: Hi everyone, please I need some help on g_hbond. I concatenated 3 trajectories. I ran g_hbond on the concatenated trajectory. I got the result of h_bonds. Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a different result, it means: if I take the first 10ps of my concatenated trajectory and I run g_hbond on these 10ps. I get some H-bonds eg. Gly(N)...H(gly)...O but this same H-bond doesn't appear in the first 10ps of my concatenated trajectory's HBmap. Please does anyone have an idea where I might have done a mistake? Thank you, Carla The first thing to check is if you're reading the matrix upside down. Sounds trivial, but it's an eaasy mistake to do. Cheers, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_hbond on concatenated trajectory
I'm sorry I don't understand, because your last answer doesn't correspond to what's written in the manual. I'm using gromacs 4.0.3 and the manual says: -hbm: existence matrix. Ordering is identical to that in -hbn index file. And yes, my trajectory is concatenated the way I intended to, but I will check anyway. Carla On Fri, Oct 15, 2010 at 1:23 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Carla Jamous skrev 2010-10-15 12.05: Hi everyone, please I need some help on g_hbond. I concatenated 3 trajectories. I ran g_hbond on the concatenated trajectory. I got the result of h_bonds. Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a different result, it means: if I take the first 10ps of my concatenated trajectory and I run g_hbond on these 10ps. I get some H-bonds eg. Gly(N)...H(gly)...O but this same H-bond doesn't appear in the first 10ps of my concatenated trajectory's HBmap. Please does anyone have an idea where I might have done a mistake? Thank you, Carla Have you confirmed that the concaternation was done the way you intended? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Percentage of H-bonds
Thank you Justin,
you Perl script has been a great help!
Cheers,
Carla
On Mon, Oct 11, 2010 at 4:31 PM, Justin A. Lemkul jalem...@vt.edu wrote:
I wrote a Perl script to do a similar task (appended below). Perhaps it
will be useful to you. I hope it works; I had to hack out some things that
were specific to my needs and have done only limited testing.
-Justin
#!/usr/bin/perl
#
# plot_hbmap.pl - plot the probability of finding a particular hydrogen
bond
# based on several input files:
# 1. coordinate file (for atom naming) - MUST be a .pdb file with NO
CHAIN IDENTIFIERS
# 2. hbmap.xpm
# 3. hbond.ndx (modified to contain only the atom numbers in the
[hbonds...] section, nothing else)
#
use strict;
unless(@ARGV) {
die Usage: perl $0 -s structure.pdb -map hbmap.xpm -index hbond.ndx\n;
}
# define input hash
my %args = @ARGV;
# input variables
my $map_in;
my $struct;
my $ndx;
if (exists($args{-map})) {
$map_in = $args{-map};
} else {
die No -map specified!\n;
}
if (exists($args{-s})) {
$struct = $args{-s};
} else {
die No -s specified!\n;
}
if (exists($args{-index})) {
$ndx = $args{-index};
} else {
die No -index specified!\n;
}
# open the input
open(MAP, $map_in) || die Cannot open input map file!\n;
my @map = MAP;
close(MAP);
open(STRUCT, $struct) || die Cannot open input coordinate file!\n;
my @coord = STRUCT;
close(STRUCT);
open(NDX, $ndx) || die Cannot open input index file!\n;
my @index = NDX;
close(NDX);
# determine number of HB indices and frames
my $nres = 0;
my $nframes = 0;
for (my $i=0; $iscalar(@map); $i++) {
if ($map[$i] =~ /static char/) {
my $res_line = $map[$i+1];
my @info = split( , $res_line);
$nframes = $info[0];
my @nframes = split('', $nframes);
shift(@nframes);# get rid of the
$nframes = join('', @nframes);
$nres = $info[1];
}
}
print Processing the map file...\n;
print There are $nres HB indices.\n;
print There are $nframes frames.\n;
# initialize hashes for later output writing
# counter $a holds the HB index from hbond.ndx
my %hbonds;
for (my $a=0; $a$nres; $a++) {
$hbonds{$a+1} = 0;
}
# donor/acceptor hashes for bookkeeping purposes
my %donors;
for (my $b=1; $b=$nres; $b++) {
$donors{$b} = 0;
}
my %acceptors;
for (my $c=1; $c=$nres; $c++) {
$acceptors{$c} = 0;
}
# clean up the output - up to 18 lines of comments, etc.
splice(@map, 0, 18);
# remove any x-axis or y-axis lines
for (my $n=0; $nscalar(@map); $n++) {
if (($map[$n] =~ /x-axis/) || ($map[$n] =~ /y-axis/)) {
shift(@map);
$n--;
}
}
# There should now be $nres lines left in the file
# The HB map for the last index is written first (top-down in .xpm file)
# * Element 0 is index $nres, element 1 is $nres-1, etc.
for (my $i=$nres; $i=1; $i--) {
# There will be $nframes+2 elements in @line (extra two are at
beginning
# and end of the line)
# Establish a conversion factor and split the input lines
my $j = $nres - $i;
my @line = split('', $map[$j]);
# for each index, write to hash
for (my $k=1; $k=($nframes+1); $k++) {
if ($line[$k] =~ /o/) {
$hbonds{$i}++;
}
}
}
print Processing the index file...\n;
# Open up the index file and work with it
for (my $n=0; $n$nres; $n++) {
my @line = split( , $index[$n]);
$donors{$n+1} = $line[0];
$acceptors{$n+1} = $line[2];
}
# some arrays for donor and acceptor atom names
my @donor_names;
my @donor_resn;
my @acceptor_names;
my @acceptor_resn;
# Open up the structure file and work with it
print Processing coordinate file...\n;
foreach $_ (@coord) {
my @line = split( , $_);
my $natom = $line[1];
my $name = $line[2];
my $resn = $line[3];
my $resnum = $line[4];
if ($line[0] =~ /ATOM/) {
unless ($resn =~ /SOL/) {
for (my $z=1; $z=$nres; $z++) {
if ($donors{$z} == $natom) {
$donor_names[$z] = $name;
$donor_resn[$z] = join('', $resn, $resnum);
} elsif ($acceptors{$z} == $natom) {
$acceptor_names[$z] = $name;
$acceptor_resn[$z] = join('', $resn, $resnum);
}
}
}
}
}
# open a single output file for writing
open(OUT, summary_HBmap.dat) || die Cannot open output file!\n;
printf(OUT %10s\t%10s\t%10s\t%10s\%10s\n, #Donor, , Acceptor,
, % Exist.);
for (my $o=1; $o=$nres; $o++) {
printf(OUT %10s\t%10s\t%10s\t%10s\t%10.3f\n, $donor_resn[$o],
$donor_names[$o], $acceptor_resn[$o], $acceptor_names[$o],
(($hbonds{$o}/$nframes)*100));
}
close(OUT);
exit;
Carla Jamous wrote:
Hi everyone,
I tried to analyze the H-bonds in my trajectory with g-hbond and I
analysed the xpm and ndx file. But now I need to know the percentage of
existence of each hbond during
[gmx-users] Percentage of H-bonds
Hi everyone, I tried to analyze the H-bonds in my trajectory with g-hbond and I analysed the xpm and ndx file. But now I need to know the percentage of existence of each hbond during my trajectory. Is there a way to do it with a command line? Or is there a program (someone told me there are python programs for analysis of gromacs trajectories) to extract this information from the .xpm file? Thank you. Cheers, 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] xpm file
Thank you Justin, I used an .m2p file to change the properties of my .xpm. I got an .eps file that I opened with Gimp. In order to visualize this .eps file, I have to put 200% in Gimp. But my problem is that my graph is too large, so I can't seem to print it out. I really to print the .eps file, so please is there a way to do it or do I have to split my trajectory and generate many .eps ? Thanks, Carla On Fri, Oct 1, 2010 at 2:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, Please I need some help visualizing an .xpm file. I tried to open my .xpm file (g_hbond matrix) with Gimp but It gives me red lines that I don't understand. So I converted my .xpm file into an .eps file with xpm2ps. When I try to open my .eps file, I get the legend: Hydrogen bonds white=none red=Present And the legend of my axis: x axis=time(ps) y axis=Hydrogen Bond index But I can't see the values: It means I see that there is an axis but it's a black bold line instead of values of time or number of atoms in hydrogen bonds. You're not going to get any numbers in this plot (aside from hydrogen bond indices). The matrix you're trying to plot is an existence matrix, a red pixel if the hydrogen bond is present, a white one if none is present. You can map which hydrogen bond is which from the hbond.ndx file. That is, once you get it rendered properly (see below). Please how can I visualize correctly my matrix? You can alter its properties (proportions, x/y spacing) with a .m2p file. There is an example in the online manual. If the plot is simply a straight line, you'll probably want to decrease the x-spacing and increase the y-spacing to make it look normal. -Justin Thank you Carla -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] xpm file
Hi everyone, Please I need some help visualizing an .xpm file. I tried to open my .xpm file (g_hbond matrix) with Gimp but It gives me red lines that I don't understand. So I converted my .xpm file into an .eps file with xpm2ps. When I try to open my .eps file, I get the legend: Hydrogen bonds white=none red=Present And the legend of my axis: x axis=time(ps) y axis=Hydrogen Bond index But I can't see the values: It means I see that there is an axis but it's a black bold line instead of values of time or number of atoms in hydrogen bonds. Please how can I visualize correctly my matrix? Thank you 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] trjconv -pbc
Hi everyone, please I'm doing a simulation of a dimer with a ligand. When I want to visualize my trajectory, I have the problem that my dimer or my ligand or both diffuse out of the box and I don't have a continuous trajectory. I tried many options: 1)trjconv -center -pbc mol -ur compact (centering on protein) 2) trjconv -center -pbc mol (centering on the ligand) 3) trjconv -center -pbc atom (centering on ligand) and then, trjconv -pbc whole 4) trjconv -pbc nojump and then trjconv -fit rot+trans 5) trjconv -center -pbc mol (centering on protein) and then trjconv -fit rot+trans 6) trjconv -center -pbc mol -ur compact (centering on ligand) and then -fit rot+trans *all of these options didn't work* I tried a last one: trjconv -center -pbc atom -ur compact (centering on ligand) and then trjconv -pbc nojump and then trjconv -fit rot+trans this one is the best one but I still have one part of my molecule that diffuses out of the box at one point in my trajectory. Please I'm out of ideas, can anyone give me a hint on how to get a fully continuous trajectory entirely centered in my box? Thank you 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Protein out of the box (not PBC problem)
Hi everyone, please I can't figure out how to do this: I have a trajectory with water. If I concatenate it, since I have a FAT32 file system, it's a file too large! So I'm trying to avoid this. For that, I extracted my protein (it's a dimer) from each step of my simulation (when doing that, I did -pbc nojump and then I fit) and then concatenated all the steps, to obtain the whole trajectory with only the protein. When I watch my trajectory with VMD, I suspect that the distance between the monomers is larger than the dimension of my box. I'm sure that it's not a PBC problem, because I already did trjconv -pbc nojump. So my question is: is there a way to check if my protein is coming out of the box, without having to watch the whole trajectory with water molecules, because I can't do that. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] incomplete frame
Thank you Justin for your advice, I did gmxcheck on the non-concatenated trajectory and found that my trajectory is not corrupted. I did re-run trjcat, without any problem. But when I run trjconv, it gives the same error message as before. It's really strange because I'm sure that my trajectory is ok (with gmxcheck)! Please do you have another idea? Thanks, Carla On Thu, Sep 2, 2010 at 3:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I concatenated many trajectories with trjcat and didn't have any problem. But when I did trjconv, I had this warning: WARNING: Incomplete frame: nr 6077 time 12154 so I tried to do gmxcheck on my concatenated .xtc and got : Reading frame 0 time0.000 # Atoms 192409 Precision 0.001 (nm) Reading frame6000 time 12000.001 WARNING: Incomplete frame: nr 6077 time 12154 Item#frames Timestep (ps) Step 60772 Time 60772 Lambda 0 Coords60772 Velocities 0 Forces 0 Box 60772 please can anyone tell me what might be the problem, knowing that when I gmxcheck the file .xtc that contains this frame, I don't get a warning. Two possibilities: 1. trjcat corrupted the frame when trying to write the full trajectory 2. The original non-concatenated trajectory is corrupted and trjcat passed over the problem, while trjconv cannot. Check the original (non-concatenated) trajectories to assess their integrity. If #1 is true, run trjcat again. If #2 is true, you cannot use the corrupted frame(s), which may mean re-running from a point prior to the corruption. -Justin Thank you, Carla -- 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 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] incomplete frame
I didn't un out of disk space but the size of my concatenated .xtc file is 4 GB. Why? the size of my file affects trjconv? Carla On Fri, Sep 3, 2010 at 10:35 AM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Carla Jamous carlajam...@gmail.com Date: Friday, September 3, 2010 18:31 Subject: Re: [gmx-users] incomplete frame To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Thank you Justin for your advice, I did gmxcheck on the non-concatenated trajectory and found that my trajectory is not corrupted. I did re-run trjcat, without any problem. But when I run trjconv, it gives the same error message as before. It's really strange because I'm sure that my trajectory is ok (with gmxcheck)! Please do you have another idea? Have you run out of disk space, or run into a 2GB file size limit? Mark Thanks, Carla On Thu, Sep 2, 2010 at 3:07 PM, Justin A. Lemkul jalem...@vt.eduwrote: Carla Jamous wrote: Hi everyone, I concatenated many trajectories with trjcat and didn't have any problem. But when I did trjconv, I had this warning: WARNING: Incomplete frame: nr 6077 time 12154 so I tried to do gmxcheck on my concatenated .xtc and got : Reading frame 0 time0.000 # Atoms 192409 Precision 0.001 (nm) Reading frame6000 time 12000.001 WARNING: Incomplete frame: nr 6077 time 12154 Item#frames Timestep (ps) Step 60772 Time 60772 Lambda 0 Coords60772 Velocities 0 Forces 0 Box 60772 please can anyone tell me what might be the problem, knowing that when I gmxcheck the file .xtc that contains this frame, I don't get a warning. Two possibilities: 1. trjcat corrupted the frame when trying to write the full trajectory 2. The original non-concatenated trajectory is corrupted and trjcat passed over the problem, while trjconv cannot. Check the original (non-concatenated) trajectories to assess their integrity. If #1 is true, run trjcat again. If #2 is true, you cannot use the corrupted frame(s), which may mean re-running from a point prior to the corruption. -Justin Thank you, Carla -- 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://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 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] incomplete frame
Hi everyone, I concatenated many trajectories with trjcat and didn't have any problem. But when I did trjconv, I had this warning: WARNING: Incomplete frame: nr 6077 time 12154 so I tried to do gmxcheck on my concatenated .xtc and got : Reading frame 0 time0.000 # Atoms 192409 Precision 0.001 (nm) Reading frame6000 time 12000.001 WARNING: Incomplete frame: nr 6077 time 12154 Item#frames Timestep (ps) Step 60772 Time 60772 Lambda 0 Coords60772 Velocities 0 Forces 0 Box 60772 please can anyone tell me what might be the problem, knowing that when I gmxcheck the file .xtc that contains this frame, I don't get a warning. Thank you, 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
[gmx-users] g_covar
Hi everyone, please I'm using gromacs 4.0.3, and I want to see the program g_covar, except that I have it in binary file and I want to see the C program in text format. Please how can I have access to it? Thank you 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
[gmx-users] Dimer g_rms
Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole dimer. However, when I run g_rmsd on Calpha, but this time, to get the RMSD of one chain (one monomer), the graph is constant with value around 1 A. and this for both chains, when taken alone. In this case, I take a .tpr file, a .xtc file and a .ndx file of the monomer. So is this an error of using g_rms? Thank you. 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] Dimer g_rms
Thank you for all your replies. Actually, I have already applied trjconv -pbc. So I'm sure that my analysis is on a whole protein, centered in my box. I'm using gromacs 4.0.3 So I think that you were right by saying that my dimer is not stable while my monomers are. But now, I have to fgure out why. Thanks again, Carla On Wed, Jun 30, 2010 at 1:54 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, Not necessary! If the dimer separates across the boundaries you have a problem of fitting the two together while they are separated. This is only if you use the dimer. The monomers would be fine. That was the case before gromacs 4. But the current versions don't keep molecules whole. This means that a PBC effect will show up in at least one monomer, if there is splitting over the boundaries. It also means that the jumps due to this are much smaller, and may not be as easily identified as before. That's a general word of caution, unrelated to the issue mentioned here. Concluding, if the version is 4, the increase in RMSD may either be due to splitting or due to relative motion of the domains, but the evolution of the RMSD (sudden or gradual) will tell which is the case. Otherwise, the increase will be due to relative motion of the domains. 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 -- 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] g_anaeig -proj
Hi everyone, please I'm doing for the first time a covariance analysis. I followed this tutorial: http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.htmlhttp://nmr.chem.uu.nl/%7Etsjerk/course/molmod/analysis1.html But I don't understand. -proj gives the projection of the trajectory on the first eigenvector, so I was expecting to have new coordinates for each atom or each residue. Instead, I get a .xvg file saying: projection on eigenvectors (nm) @ xaxis label Time (ps) yaxis label vec 1 Please can anyone tell me what this actually means? What data is in nanometers? What does gromacs project? Sorry if my question is stupid, but I can't find the answer. Thank you. 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
[gmx-users] covariance analysis?
Hi everyone, please I have a kind of theoretical question. I want to figure out if there's an allosteric relation between my ligand an a secondary structure (a loop or a helix) in my protein: if there motions are correlated. Is it possible to do that with a covariance analysis? 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
[gmx-users] xpm file
Hi everyone, please it's been two days that I can't have access to search the mailing list. Maybe there is a problem. So please can anyone help me? I used the g_covar and got covar.xpm file. My problem is that I can't figure out which application can open the xpm file, so I converted it to .eps file opened it with Gimp, but the quality of the colours is really bad so I can't see much to analyse the graph. Please has anyone encountered this problem before? 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 Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs? Cheers, Carla On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: 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 -- 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
Please does anyone know how is calculated the B factor in gromacs? What is the formula that gives the B factor with the average coordinates with g_rmsf? Carla On Fri, Jun 11, 2010 at 10:53 AM, Erik Marklund er...@xray.bmc.uu.sewrote: Hi, yes it can be done with g_covar, but such an average structure is often of little physical significace. Imagine for instance the acerage structure of a rotating methyle group (it's a bunch of atoms on a line). Erik Carla Jamous skrev: Hi Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to take 3 structures and make an average structure of these 3. Is there a way to do it with gromacs? Cheers, Carla On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar tsje...@gmail.commailto: tsje...@gmail.com wrote: Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous carlajam...@gmail.com mailto: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 mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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] 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
[gmx-users] g_energy graph .xvg
Hi everyone, please I have a practical question that may sound stupid but I can't figure out the answer. When I run g_energy I type the Energies I need, for example: 10 (Potential) 14 (Kinetic) 12 (Total) My problem is even though I get the averages of the 3 energies on my screen, I can't get the three energies on the same graph (.xvg file). Please does anyone have an idea? Thank you 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_energy graph .xvg
Thank you all, the xmgrace -nxy worked. but you're right, it's more useful to see the fluctuations. Thanks Carla On Tue, Jun 1, 2010 at 10:02 AM, Erik Marklund er...@xray.bmc.uu.se wrote: Mark Abraham skrev: - Original Message - From: Carla Jamous carlajam...@gmail.com Date: Tuesday, June 1, 2010 17:48 Subject: [gmx-users] g_energy graph .xvg To: Discussion list for GROMACS users gmx-users@gromacs.org Hi everyone, please I have a practical question that may sound stupid but I can't figure out the answer. When I run g_energy I type the Energies I need, for example: 10 (Potential) 14 (Kinetic) 12 (Total) My problem is even though I get the averages of the 3 energies on my screen, I can't get the three energies on the same graph (.xvg file). Well they have wildly different values, so plotting all three together means you can't see any fluctuations, so you might as well just look at the averages... If you want all three with fluctuations, then you'll need to play with the plotting program's functionality for representations and axes (for xmgrace). See http://www.gromacs.org/Documentation/How-tos/Graphing_Data for various ideas on plotting. Mark Zooming is of course an option. I for one find it helpful to inspect the energies as a function of time to get an idea of the convergence time for certain properties and to detect any wierdness in my setup that may have ruined my simulations. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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] tpr file
Hi everyone, please I have an important question: When I continue my simulation, I do: tpbconv -s .tpr -extend-s .tpr mdrun -v -s .tpr -cpi .cpt -cpo .cpt -o .trr -c .gro -x .xtc -e .edr -g .log At one point of my simulation, I had a problem, the directory that contains all my topology and parameter files has been deleted. So does it affect my simulation? Does gromacs need the topology and parameters at each step or does it stock all of these in the .tpr file? Thank you 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
[gmx-users] Essential Dynamics
Hi everyone, Please I need a piece of information not related to gromacs. I'm searching for a document or article that may explain Essential Dynamics to beginners. 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
[gmx-users] Potential Energy problem
Hi everyone, please I encountered a problem of potential energy rising suddenly during my simulation. Someone advised me to take the previous conformation of my system, center it in the box, minimize it then restart my MD simulation, by taking the previous velocities of this conformation. So I did the centering and the minimization. Usually, I used to do the following for my MD run. tpbconv -s .tpr -extend 6000 -o .tpr mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc -e .edr -g .log However, this time I need to go from the minimized structure. So in order to get a .tpr file of my minimized structure (.gro), I created a .mdp file with gen_vel=no and did: grompp -f .mdp -c minimized.gro -p .top -o minimized.tpr After that, I tried the following: tpbconv -s minimized.tpr -extend 6000 -o .tpr mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc -e .edr -g .log and got this error message: *WARNING: This run will generate roughly 3410368410012306432 Mb of data starting mdrun 'Protein in water' 6 steps, 12.0 ps (continuing from step 27, 54.0 ps). nodetime = 0! Infinite Giga flopses! Parallel run - timing based on wallclock.* Please does anyone have a solution? 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] Potential Energy problem
Thank you Mark, I'm running gromacs 4.0.3., so I don't know if I should submit a bugzilla. Please Do you know another way to restart my MD run? Thanks, Carla On Tue, May 11, 2010 at 1:00 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/05/2010 7:55 PM, Carla Jamous wrote: Hi everyone, please I encountered a problem of potential energy rising suddenly during my simulation. Someone advised me to take the previous conformation of my system, center it in the box, minimize it then restart my MD simulation, by taking the previous velocities of this conformation. So I did the centering and the minimization. Usually, I used to do the following for my MD run. tpbconv -s .tpr -extend 6000 -o .tpr mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc -e .edr -g .log However, this time I need to go from the minimized structure. So in order to get a .tpr file of my minimized structure (.gro), I created a .mdp file with gen_vel=no and did: grompp -f .mdp -c minimized.gro -p .top -o minimized.tpr After that, I tried the following: tpbconv -s minimized.tpr -extend 6000 -o .tpr mdrun -v -s .tpr -cpi state_.cpt -cpo state_.cpt -o .trr -c .gro -x .xtc -e .edr -g .log and got this error message: *WARNING: This run will generate roughly 3410368410012306432 Mb of data starting mdrun 'Protein in water' 6 steps, 12.0 ps (continuing from step 27, 54.0 ps). That looks like a bug. The run time from your .mdp+tpbconv is 12ps, but the .cpt is already past that and GROMACS is using integer arithmetic inappropriately to get a huge number of steps (thus large output volume estimate) but no actual steps occur. If you're running GROMACS 4.0.7, please submit a bugzilla. Mark -- 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] H-bonds
Hi, please I'm trying to measure an hbond between 2 specific atoms. When I used g_hbond I didn't the result I expected because it doesn't specify the atoms that constitute the H bond. Now I'm trying with g_dist but I encountered a problem: when I do the following in my index file: r 172 a HD2 it tells me: empty group So please can anyone help me? Thank you. 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
[gmx-users] Extending simulations
Hi everyone, It's the first I use the process of extending simulations. I did the following: tpbconv -s prot.tpr -extend 6000 -o protein.tpr mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr -c protein.gro -x protein.xtc -e md.edr -g md.log But I noticed sthg strange: gromacs named my files: protein.part0002.gro/.xtc/.trr/.log/.edr Please does anyone know why it did this? 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
[gmx-users] gen_vel error
Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log But in my em.mdp, I kept: gen_vel = yes So is my simulation correct or does it generate velocities each time? I mean, what is meaningful: gen_vel or grompp -t -e ? Thank you 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
[gmx-users] g_rms warning
Hi everyone, please I just need a precision: I need to calculate the RMSD of a trajectory by comparing it to a reference structure that doesn't have the same number of atoms. Gromacs is calculating the RMSD, but meanwhile it generates this warning:topology has 4839 atoms, whereas trajectory has 4834 Does it really affect the result of my RMSD or can I ignore it? 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
[gmx-users] pdb gro files
Hi, please I'm having a problem while running a minimisation. I prepared my system with pdb2gmx and generated .pdb files. From the last pdb file, I did grompp generated the tpr file that I used to start my minimization. At the 46th step, I encountered the problem:water molecule cannot be settled. I looked at the pdb file and found that many water residues have the same number because above residue , it restarts to count residue 0, 1, etc... I prepared the same system but I generated .gro files instead of .pdb started my minimization. But did't encounter the same problem. I looked at the gro file here, it's the atomic number that can't be above 9. So did anyone encounter this problem before, if yes, please do you have a solution to propose? 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] value of an angle
Thank you for your replies, indeed it worked! But now, I'm looking for a command line that allows me to calclulate the RMSF (or if you prefer, the distance between Calpha) between 2 static structures. Carla On Thu, Feb 25, 2010 at 11:55 AM, Amir Marcovitz amarcov...@gmail.comwrote: Hi, if you are interested in a particular angle (between a triad of atoms) you can specify it in angle.ndx file (to generate the angles run: mk_angndx -s topol.tpr -n angle.ndx) the -ov flag of g_angle will generate the angle trajectory and the -od flag will generate its distribution cheers On Wed, Feb 24, 2010 at 10:22 PM, Carla Jamous carlajam...@gmail.comwrote: Hi everyone, please I'm trying to find a way to calculate the value of an angle during the time of my simulation. g_angle calculates a distribution or an average. 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 -- 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] value of an angle
Hi everyone, please I'm trying to find a way to calculate the value of an angle during the time of my simulation. g_angle calculates a distribution or an average. 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
[gmx-users] ffamber94 with gromacs 4.0.3
Hi, please does anyone know if the ffamber94 force-field is compatible with gromacs version 4.0? Because I used to use it with gromacs 3.3.3 but now that I'm trying with gromacs 4, I'm having some error messages. Thank you 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] pbc whole
Hi, Actually, the ligand I'm using is an ATP molecule, and from the beginning, ATP is not bound to my protein by a chemical bond. It is just crystallized with my protein. I checked with genconf now I'm certain that my ATP molecule is still with the protein, but why trjconv doesn't work why I can't get my ATP molecule to stay within the box I'm looking at? Thanks, Carla On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi Justin, Thank you for your answer but I'm still not getting my ligand to stay in the box. I tried the following(after taking a look at the mailing list archive): trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans So please do you have another advise to give me? If that's not working, then I wonder if your ligand is still actually bound to your protein :) The above sequence always works for me, as long as there actually is a complex. You can also try -pbc cluster, but I know that algorithm can hang. -Justin Thanks Carla On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc grps outtrj Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD. the -pbc whole fixed it. However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value? You may need several more iterations of trjconv (one rarely does the trick), employing -pbc nojump, -pbc cluster, and/or -center. For protein-ligand complexes, I have often found that the combination of: trjconv -pbc mol -ur compact -center (centering on Protein) does the trick. And it makes molecules whole, as well :) I think there are also some breakdowns (documented somewhere in the list archive) when applying -fit and -pbc in the same step. I believe it is recommended to fix PBC first, then applying any sort of fitting in a separate, subsequent step. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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] pbc whole
Hi Tsjerk, sorry I didn't understand this part of your explanation:Can you make an image of the last frame and send a link to it? But anyhow, please can you send me the version of trjconv that does the trick? Thanks, Carla On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Carla, I checked with genconf now I'm certain that my ATP molecule is still with the protein That's good to know :) trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) So what did come out of this then? It should have given you a compact representation of your system with the protein in the center. But if the protein's in the center and everything is put as close to that center as possible, which is what compact does, then the ATP should be there too. Can you make an image of the last frame and send a link to it? Alternatively, I have a patched version of trjconv that you can use to do the trick. I can send it if you want. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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
Re: [gmx-users] pbc whole
Hi Justin and Tsjerk, Thank you for your answers, but I found a command that worked for me:) First, I concatenated the ensemble of my trajectory. then, I did the following: trjconv -s a.tpr -f traj.xtc -o traj1.xtc -pbc nojump -n b.ndx Cheers, Carla On Thu, Feb 18, 2010 at 12:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi Tsjerk, sorry I didn't understand this part of your explanation:Can you make an image of the last frame and send a link to it? Render an image of your system from the end of your trajectory and post it somewhere online (like photobucket); do not send it as an attachment to your email. -Justin But anyhow, please can you send me the version of trjconv that does the trick? Thanks, Carla On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar tsje...@gmail.commailto: tsje...@gmail.com wrote: Hi Carla, I checked with genconf now I'm certain that my ATP molecule is still with the protein That's good to know :) trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) So what did come out of this then? It should have given you a compact representation of your system with the protein in the center. But if the protein's in the center and everything is put as close to that center as possible, which is what compact does, then the ATP should be there too. Can you make an image of the last frame and send a link to it? Alternatively, I have a patched version of trjconv that you can use to do the trick. I can send it if you want. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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] pbc whole
Hi Justin, I'm still trying to figure out what happened with my ligand. Meanwhile, I have another question: I can't figure out how to calculate an average structure in gromacs. And does g_rmsf calculate the average structure automatically? Thanks again Carla On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi Justin, Thank you for your answer but I'm still not getting my ligand to stay in the box. I tried the following(after taking a look at the mailing list archive): trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans So please do you have another advise to give me? If that's not working, then I wonder if your ligand is still actually bound to your protein :) The above sequence always works for me, as long as there actually is a complex. You can also try -pbc cluster, but I know that algorithm can hang. -Justin Thanks Carla On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc grps outtrj Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD. the -pbc whole fixed it. However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value? You may need several more iterations of trjconv (one rarely does the trick), employing -pbc nojump, -pbc cluster, and/or -center. For protein-ligand complexes, I have often found that the combination of: trjconv -pbc mol -ur compact -center (centering on Protein) does the trick. And it makes molecules whole, as well :) I think there are also some breakdowns (documented somewhere in the list archive) when applying -fit and -pbc in the same step. I believe it is recommended to fix PBC first, then applying any sort of fitting in a separate, subsequent step. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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] pbc whole
Thank you Tsjerk, but one more question: if I do the following: g_rmsf -f a.xtc -s b.tpr -o rmsf.xvg -ox average.pdb -n c.ndx does gromacs claculate the rmsf after fitting to b.tpr or to average.pdb? if I want it to calculatefluctuations between the position of particle i and the time-averaged position of the same particle i, do I have to do: g_rmsf -f a.xtc -s average.pdb -o rmsf.xvg? Thank you sorry to bother. I'm just trying to understand what g_rmsf really does, to help me analyze my results. Carla On Wed, Feb 17, 2010 at 10:25 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Carla, Justin's recipe should've worked. As he suggested, maybe the ligand is not with the protein. You can check by multiplying your system with genconf: genconf -f in.pdb -o out.pdb -nbox 2 2 2 If the ligand is with the protein, one copy will be located in one of the copies of the protein. g_rmsf does write the average structure, if requested. Use the option -ox Cheers, Tsjerk On Wed, Feb 17, 2010 at 10:08 AM, Carla Jamous carlajam...@gmail.com wrote: Hi Justin, I'm still trying to figure out what happened with my ligand. Meanwhile, I have another question: I can't figure out how to calculate an average structure in gromacs. And does g_rmsf calculate the average structure automatically? Thanks again Carla On Tue, Feb 16, 2010 at 5:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi Justin, Thank you for your answer but I'm still not getting my ligand to stay in the box. I tried the following(after taking a look at the mailing list archive): trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans So please do you have another advise to give me? If that's not working, then I wonder if your ligand is still actually bound to your protein :) The above sequence always works for me, as long as there actually is a complex. You can also try -pbc cluster, but I know that algorithm can hang. -Justin Thanks Carla On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc grps outtrj Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD. the -pbc whole fixed it. However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value? You may need several more iterations of trjconv (one rarely does the trick), employing -pbc nojump, -pbc cluster, and/or -center. For protein-ligand complexes, I have often found that the combination of: trjconv -pbc mol -ur compact -center (centering on Protein) does the trick. And it makes molecules whole, as well :) I think there are also some breakdowns (documented somewhere in the list archive) when applying -fit and -pbc in the same step. I believe it is recommended to fix PBC first, then applying any sort of fitting in a separate, subsequent step. -Justin Thank you Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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
[gmx-users] Average structure -s
Hi everyone, please I need to calculate RMSF after fitting to the average structure of my MD simulation. Can anyone tell me how to do that? (especially, how to calculate the average structure) Another question that may sound stupid: does the -s have the same function with trjconv g_rmsf? Can anyone clarify this option for me? Thank you 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] pbc whole
Hi Justin, Thank you for your answer but I'm still not getting my ligand to stay in the box. I tried the following(after taking a look at the mailing list archive): trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering on Protein) trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans So please do you have another advise to give me? Thanks Carla On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc grps outtrj Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD. the -pbc whole fixed it. However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value? You may need several more iterations of trjconv (one rarely does the trick), employing -pbc nojump, -pbc cluster, and/or -center. For protein-ligand complexes, I have often found that the combination of: trjconv -pbc mol -ur compact -center (centering on Protein) does the trick. And it makes molecules whole, as well :) I think there are also some breakdowns (documented somewhere in the list archive) when applying -fit and -pbc in the same step. I believe it is recommended to fix PBC first, then applying any sort of fitting in a separate, subsequent step. -Justin Thank you Carla -- 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 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] Average structure -s
I looked at g_rmsf -h but the problem is that it's not clear enough. The help doesn't state how g_rmsf works what does it calculate exactly. Because the definition of an RMSF is the following: the mean-square fluctuation is a measure of the deviation between the position of particle i and some reference position. Typically, this reference position will be the time-averaged position of the same particle i. So does g_rmsf calculate the average structure then the RMSF according to this average structure? Or does it calculate the RMSF after fitting to a reference structure that I would have specified with the option -s? Thanks Carla On Tue, Feb 16, 2010 at 3:54 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 17/02/10 01:12, Carla Jamous wrote: Hi everyone, please I need to calculate RMSF after fitting to the average structure of my MD simulation. Can anyone tell me how to do that? (especially, how to calculate the average structure) g_rmsf. There's a section in the manual that gives a breakdown of the GROMACS tools by topic that can help guide you. Another question that may sound stupid: does the -s have the same function with trjconv g_rmsf? Can anyone clarify this option for me? Use the -h flag to the tool to see a description of how things work. Mark -- 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] pbc whole
Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc grps outtrj Before, I had a problem with residues of my protein showing at the other end of the box, when I display my .xtc with VMD. the -pbc whole fixed it. However, now I have another issue: my ligand is at the other end of the box. So please can anyone tell me what can I do to fix that and get a reasonable RMSD value? Thank you 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
[gmx-users] Structure deformation
Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. What may be the problem? Thank you 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] Structure deformation
Thank you Justin, you were right I was looking at the wrong residue numbers. I have another question that may also sound stupid, but I can't figure it out: I want to extract from my trajectory, the protein, the ligand and ions. However, when I try to do that with trjconv -f .trr -s .trr -n .ndx gromacs asks to choose a group from my index file. But if I choose group 0 1 2 it only takes the first group without the rest. So how can I extract many groups at once from my trajectory? Carla On Fri, Jan 29, 2010 at 12:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi everyone, I have a question about structure deformation Can pdb2gmx alter secondary structures of my protein, while adding hydrogens. Because I had a helix in my protein, that became a beta-sheet after pdb2gmx. Sorry to say, but this sounds completely unlikely. A bug of this magnitude surely would've been noticed long ago. What may be the problem? Are you certain you're looking at the same residues? pdb2gmx renumbers from 1, so if there are missing N-terminal residues, they will not have the same numbers before and after pdb2gmx. -Justin Thank you Carla -- 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 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] xtc file
Hi everyone, Please I'm having a problem with mdrun: If I type: mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g test.log I never get the .xtc file. Can anyone tell me why what can I do to have an .xtc file? Thank you 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] xtc file
Thank you . Carla On Tue, Jan 26, 2010 at 11:53 AM, Carsten Kutzner ckut...@gwdg.de wrote: On Jan 26, 2010, at 11:48 AM, Carla Jamous wrote: Hi everyone, Please I'm having a problem with mdrun: If I type: mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g test.log I never get the .xtc file. Can anyone tell me why what can I do to have an .xtc file? In your input .mdp file you have to set nstxtcout to something larger than 0. Carsten-- 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] Load imbalance
Hi everyone, Lately I've been using gromacs version 3.3.3. Yesterday, I started simulations in a cluster where gromacs version is 4.0.3. After a run, I got this error message: Average load imbalance: 0.5 % Part of the total run time spent waiting due to load imbalance: 0.3 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Average PME mesh/force load: 0.898 Part of the total run time spent waiting due to PP/PME imbalance: 2.7 % I don't have a clue what this means how can I fix it? Please can anyone help? Thank you 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] Load imbalance
Yes, but I forgot to say that I got this note that followed: 5.4 % performance was lost because the PME nodes had less work to do than the PP nodes. You might want to decrease the number of PME nodes or decrease the cut-off and the grid spacing. Carla On Fri, Jan 22, 2010 at 1:34 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Carla Jamous skrev: Hi everyone, Lately I've been using gromacs version 3.3.3. Yesterday, I started simulations in a cluster where gromacs version is 4.0.3. After a run, I got this error message: Average load imbalance: 0.5 % Part of the total run time spent waiting due to load imbalance: 0.3 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Average PME mesh/force load: 0.898 Part of the total run time spent waiting due to PP/PME imbalance: 2.7 % I don't have a clue what this means how can I fix it? Please can anyone help? Thank you Carla This is no error message. 0.5 % load imbalance just means that the workload was distributed in a good way over procesors throughout your simulation. -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- 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
Re: [gmx-users] decimal charge instead of integer
Thanks everyone, you were right, it doesn't work if I only take off one phosphate from GTP. I was using the wrong parameters, now I have an integer total charge. Carla On Thu, Jan 21, 2010 at 2:36 PM, Thomas Piggot t.pig...@bristol.ac.ukwrote: If using an amber forcefield and GTP/GDP you can use the parameters on the following website. I have used the ATP/ADP ones and have had no problems with many different systems and ATP/ADP conformations with which I used to test these parameters. http://www.pharmacy.manchester.ac.uk/bryce/amber#cof Tom Justin A. Lemkul wrote: Carla Jamous wrote: Thank you Justin, but I ran a simulation before this one with GTP it worked fine. GDP GTP parameters are identical except for GDP having less atoms. This is why I can't understand why I don't get an integer charge while I did in my previous simulation. OK, but this still doesn't help anyone give you any advice. Please refer to my previous post - which case applies to you: almost integer, or way off? It is also potentially faulty logic to suggest that GDP parameters can be generated from GTP parameters by simply chopping off a phosphate. Under most force field parameter sets, the charges on the beta-phosphate will have to change since the electronic properties of the molecule are now different. -Justin Carla On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Carla Jamous wrote: Hi, In order to run my simulation, I had to insert GDP parameters in ffamber94 (the force field I'm using). However, I'm having a problem with GDP charge. the charge of every charge group in top file should be an integer. But I'm getting a decimal charge which gives me naturally a decimal total charge of my molecule. I checked number of atoms, it's correct, their charge also. But it seems it's having trouble adding charges giving an integer charge. Does anyone have an idea where is the source of the problem? What is the charge? If it is a small difference between an integer and your charge (i.e., the difference between +1. and +2) then there is no problem. The issue there is the inherent limitation of doing a lot of floating-point operations to sum the total charge. If, however, you have a charge of +1.9256 when you wanted +2, then your parameters are simply wrong. -Justin Thanks Carla -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Thomas Piggot University of Bristol, UK. -- 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] Heating
Hi, I've been using gromacs to run some tests but it's the first time I need to heat my system very slowly, knowing that it is a quite large system. ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; title = Yo cpp = /usr/bin/cpp constraints = all-bonds constraint_algorithm = Lincs lincs_iter = 2 integrator = md dt = 0.002; ps ! nsteps = 225000; total 450 ps. nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 500 ; collect velocities every 1 ps nstfout = 0 nstlog = 50 nstenergy = 50 ; collect energies every 0.1 ps nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 vdwtype = cut-off rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes annealing = single single annealing_npoints = 10 10 annealing_time = 0 100 105 200 202 250 252 350 355 450 0 100 105 200 202 250 252 350 355 450 annealing_temp = 50 50 100 100 150 150 200 200 300 300 50 50 100 100 150 150 200 200 300 300 ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tc-grps= ProteinNon-protein tau_t = 0.10.1 ref_t = 300300 ; Energy monitoring energygrps = Protein Non-protein ; Isotropic pressure coupling is now on Pcoupl = no Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Please can anyone tell me if my mdp file is correct? I have a serious doubt about gen_temp Tcoupling. 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
[gmx-users] occupancy
Hi, I'm encountering a problem with pdb2gmx occupancy. I searched the mailing list followed this advice: do NOT throw away crystallographic water molecules before you run genbox. I kept my pdb's water mlolecules ran pdb2gmx. But still I get this warning: there were 0 atoms with zero occupancy and 1 atoms with occupancy unequal to one (out of 2658 atoms). Check your pdb file. What can I do to stop having this warning? 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] Density
Thank you Mark, for your answer. This time I have another issue: temperature. What are the ways to control temperature in gromacs (during heating or equilibration phases), other than temperature coupling? Thank you Carla On Thu, Jan 14, 2010 at 10:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Carla Jamous wrote: Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. Those tools report density-related quantities, they do not control it. However, when I use g_energy, in my list, Density doesn't appear. g_energy doesn't report the density if you have a constant-volume simulation (but grompp probably reported it when you generated the .tpr) Else, if I use g_density, it needs a file traj.xtc which I don't have. Per Erik's point, you can usually use any coordinate file or trajectory file. Mark So please can anyone tell me how to check my system's density in gromacs? Thank you 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 -- 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] Density
Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. However, when I use g_energy, in my list, Density doesn't appear. Else, if I use g_density, it needs a file traj.xtc which I don't have. So please can anyone tell me how to check my system's density in gromacs? Thank you 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
[gmx-users] add heavy atoms
Hello everyone, I need a precision, concerning gromacs. In my pdb file, some heavy atoms are missing but I need them for my simulation. So my question is: is there an application in gromacs, that can add automatically these heavy atoms? If not, does anyone have an idea of how can I do this? PS: I'm using ffamber94 with gromacs. 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] add heavy atoms
Thank you Mark One last question: is there a certain molecule builder (open-source) you recommand.? Because all the molecule builders I found, draw molecules from scratch, but what I need is to add heavy atoms to the pdb structure I already have. Carls On Fri, Jan 8, 2010 at 8:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote: Carla Jamous wrote: Hello everyone, I need a precision, concerning gromacs. In my pdb file, some heavy atoms are missing but I need them for my simulation. So my question is: is there an application in gromacs, that can add automatically these heavy atoms? If not, does anyone have an idea of how can I do this? It's outside the scope of GROMACS. If it's just an atom or two, then building them in with any old molecule builder is probably acceptable. If it's a whole loop missing, then some more high-tech might be in order. Google MODELLER and links on their webpage. There are certainly web-servers out there that will be able to do things for you, but caveat emptor. Mark -- 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] minimum residue distances
Hi everyone, since i'm in beginner in molecular dynamics, I still have some trouble with finding the adequate formulas. Now, I'm trying to find the formula to calculate the minimum residue distances. I didn't find it in Gromacs manual, so please does anyone have an idea? 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
[gmx-users] Bond paths
Hi everyone, this is a general question please does anyone know what bond paths means, and what it has to do with dihedrals? Thank you 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] Re: converting proper dihedrals into ryckaert-bellemans
Dear Alan, if I completely understood how acpypi works, it seems that it generates the topology parameters from the pdb file of the molecule. But the problem is that I have the topology parameters (my angles, bond distances and dihedrals) and want to implement them in Gromacs, so actually I want to set specific parameters' values in gromacs. Carla On Tue, Oct 20, 2009 at 5:16 PM, Alan alanwil...@gmail.com wrote: Dear Carla, Let me suggest you the wikis at acpypi.googlecode.com. And then let me ask why amber94 and not amber99sb? And why not trying acpypi in the link above as I guess it can do pretty much what you want with much less pain? Cheers, Alan On Tue, Oct 20, 2009 at 15:55, gmx-users-requ...@gromacs.org wrote: Hi everyone, I'm using the amber94 force field in gromacs. I need to add topology of a new molecule for my MD simulation. I saw this line propers treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet in my ffamber94bon.itp file. So it seems that I have to convert my proper dihedrals parameters into RB parameters, in order to run my simulation. Does anyone have an idea of how can I do this, to have the right parameters for my molecule? Thanks a lot Carla -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) ___ 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] converting proper dihedrals into ryckaert-bellemans
Hi everyone, I'm using the amber94 force field in gromacs. I need to add topology of a new molecule for my MD simulation. I saw this line propers treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet in my ffamber94bon.itp file. So it seems that I have to convert my proper dihedrals parameters into RB parameters, in order to run my simulation. Does anyone have an idea of how can I do this, to have the right parameters for my molecule? Thanks a lot 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] large VCM(group rest)
Hi, when I get the error message: water molecule cannot be settled,does it have to do with the SETTLE parameter in gromacs? If yes, does anyone know how to fix this? Carla On Thu, Oct 1, 2009 at 4:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: Carla Jamous wrote: Hi, I have a problem, I'm running EM, it works but when it comes to doing position-restrained MD, it gives me this error message: Segmentation fault Large VCM(group System): -1293135642624.0, 358859374592.0, -846768177152.0, T-cm: 6.13428e+26 I searched the archives, it says to check-out: oldwiki.gromacs.org http://oldwiki.gromacs.org but this site doesn't exist anymore. All of the content has been moved to the new site, albeit a very different organization system. You should still be able to find it with a bit of digging. So please can anyone give me the answer to this problem? The problem is that your system is suddenly moving very fast, probably blowing up. Without a further description of the system and seeing your .mdp file, it's hard to say what the root problem is. -Justin Cheers, 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 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] large VCM(group rest)
This is the mdp file i use for my energy minimization Thanks Carla ; ;1W5B all-atom ;Input file ; cpp = /usr/bin/cpp define = -DPOSRES constraints = none integrator = steep nsteps = 500 ; ;Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 nstcomm = 1 ns_type = grid nstlist = 10 nstxout = 1 rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes Tcoupl = no Pcoupl = no gen_vel = no On Fri, Oct 2, 2009 at 12:46 PM, Jochen Hub joc...@xray.bmc.uu.se wrote: Carla Jamous wrote: Hi, when I get the error message: water molecule cannot be settled,does it have to do with the SETTLE parameter in gromacs? If yes, does anyone know how to fix this? No, that probably means that you have clashes (atomic overlaps) in your system which cause huge forces. Track down which atoms cause the error message and remove the clashes. If that error message appeares during energy minimization, using flexible water may help. Define -DFLEXIBLE in the mdp file, and check in the spc/itp4p/tip3p.itp file if flexible water molecules are actually defined. Good luck, Jochen Carla On Thu, Oct 1, 2009 at 4:46 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Carla Jamous wrote: Hi, I have a problem, I'm running EM, it works but when it comes to doing position-restrained MD, it gives me this error message: Segmentation fault Large VCM(group System): -1293135642624.0, 358859374592.0, -846768177152.0, T-cm: 6.13428e+26 I searched the archives, it says to check-out: oldwiki.gromacs.org http://oldwiki.gromacs.org http://oldwiki.gromacs.org but this site doesn't exist anymore. All of the content has been moved to the new site, albeit a very different organization system. You should still be able to find it with a bit of digging. So please can anyone give me the answer to this problem? The problem is that your system is suddenly moving very fast, probably blowing up. Without a further description of the system and seeing your .mdp file, it's hard to say what the root problem is. -Justin Cheers, Carla ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto: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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org
[gmx-users] large VCM(group rest)
Hi, I have a problem, I'm running EM, it works but when it comes to doing position-restrained MD, it gives me this error message: Segmentation fault Large VCM(group System): -1293135642624.0, 358859374592.0, -846768177152.0, T-cm: 6.13428e+26 I searched the archives, it says to check-out: oldwiki.gromacs.org but this site doesn't exist anymore. So please can anyone give me the answer to this problem? Cheers, 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] water molecule cannot be settled
Hi, what do you mean: use gmxdump to trace the molecule? I'm a beginner with gromacs and all I found about gmxdump is that it reads a binary file prints that to standard output in a readable format. So how can I check if my atom number is the same in my pdb file my output file? Carla On Wed, Sep 30, 2009 at 4:38 AM, Itamar Kass itamar.k...@gmail.com wrote: Hi, another point you should consider is that the atom/molecule number in the pdb or gro file are not necessarally the what you see in your output. You should use gmxdump in such cases to trace the molecule. Cheers, Itamar --- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@med.monash.edu.au On Wed, Sep 30, 2009 at 1:14 AM, Manik Mayur manik.ma...@gmail.comwrote: 2009/9/29 Justin A. Lemkul jalem...@vt.edu Carla Jamous wrote: Thank you for your reply, but none of the water molecules with error messages is trapped inside my protein, nor is it in contact with the protein or the ions in my system. Also if the water molecules are positioned properly, you can try define = -DPOSRES_WATER in your .mdp file with a high value set in your topology(.top) file under [position restraint] section as, #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 10 10 10 #endif -Manik Then you need to watch the trajectory and see where things go wrong. In unstable systems, I often set nstxout = 1 to capture as many frames in the .trr file as possible (if the crash is happening early, as it is in your case). Likely, energy minimization did not resolve all the bad contacts, but may still have converged within your criteria. You could also specify a lower target Fmax during EM to see if things resolve. -Justin Carla On Tue, Sep 29, 2009 at 1:15 PM, Tsjerk Wassenaar tsje...@gmail.commailto: tsje...@gmail.com wrote: Hi Carla, You may have a water molecule trapped inside your protein. Check the water molecule with the given atom number in a viewer, together with your structure. If it is inside, you can try to remove it manually from the system, editing the structure file and decreasing the amount of solvent listed in te topology file. If you edit the .gro file, do mind to decrease the number on the second line (the number of atoms) by three. Hope it helps, Tsjerk On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous carlajam...@gmail.com mailto:carlajam...@gmail.com wrote: Hi, I have a problem with water molecules in my system: I'm using Gromacs with ffamber94 force-field. During minimization, I have this message: t = 0.014 ps: Water molecule starting at atom 10045 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates The minimization converged. However, molecular dynamics were stopped. I tried minimization with different parameters: Flexible, position-restrained, reducing my timestep, etc... and nothing worked. I also tried one simulation with TIP3P water model and another simulation with SPC water model and I still get the same error. I tried to access: oldwiki.gromacs.org http://oldwiki.gromacs.org but access is denied. Please does anyone have a solution to propose? Thanks Carla ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting
[gmx-users] water molecule cannot be settled
Hi, I have a problem with water molecules in my system: I'm using Gromacs with ffamber94 force-field. During minimization, I have this message: t = 0.014 ps: Water molecule starting at atom 10045 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates The minimization converged. However, molecular dynamics were stopped. I tried minimization with different parameters: Flexible, position-restrained, reducing my timestep, etc... and nothing worked. I also tried one simulation with TIP3P water model and another simulation with SPC water model and I still get the same error. I tried to access: oldwiki.gromacs.org but access is denied. Please does anyone have a solution to propose? 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] water molecule cannot be settled
Thank you for your reply, but none of the water molecules with error messages is trapped inside my protein, nor is it in contact with the protein or the ions in my system. Carla On Tue, Sep 29, 2009 at 1:15 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Carla, You may have a water molecule trapped inside your protein. Check the water molecule with the given atom number in a viewer, together with your structure. If it is inside, you can try to remove it manually from the system, editing the structure file and decreasing the amount of solvent listed in te topology file. If you edit the .gro file, do mind to decrease the number on the second line (the number of atoms) by three. Hope it helps, Tsjerk On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous carlajam...@gmail.com wrote: Hi, I have a problem with water molecules in my system: I'm using Gromacs with ffamber94 force-field. During minimization, I have this message: t = 0.014 ps: Water molecule starting at atom 10045 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates The minimization converged. However, molecular dynamics were stopped. I tried minimization with different parameters: Flexible, position-restrained, reducing my timestep, etc... and nothing worked. I also tried one simulation with TIP3P water model and another simulation with SPC water model and I still get the same error. I tried to access: oldwiki.gromacs.org but access is denied. Please does anyone have a solution to propose? 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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
