[gmx-users] parameters and restrains for Fe3+

Hi, I need to introduce new atomtypes/parameters and restrains in Gromacs for Fe3+. Could you please inform me on how can I do it? Thanks. Cheers, Carla -- View this message in context: http://gromacs.5086.n6.nabble.com/parameters-and-restrains-for-Fe3-tp4981309.html Sent from the GROMACS

[gmx-users] my e-mail to post in this list

my e-mail to post in this list is : carla.carluc...@libero.it -- 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

[gmx-users] Help with g_rmsf

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

[gmx-users] vdwtype = cut-off

= 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] g_tune_pme

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

[gmx-users] Fatal error: file type out of range (48)

$PBS_O_WORKDIR export GMXLIB=$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

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

Re: [gmx-users] Residence time and trjorder

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

[gmx-users] Residence time and trjorder

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

[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

[gmx-users] PBC

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

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

[gmx-users] Minimisation restraints

) 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

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

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

[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

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

[gmx-users] g_sas and g_rdf

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

[gmx-users] g_hbond

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

[gmx-users] g_sas resarea.xvg

@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

Re: [gmx-users] g_hbond

), 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

[gmx-users] g_hbond

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

[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

Re: [gmx-users] Percentage of H-bonds

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. Thank you. 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

Re: [gmx-users] Percentage of H-bonds

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

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

[gmx-users] g_hbond on concatenated trajectory

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

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

Re: [gmx-users] g_hbond on concatenated trajectory

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

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

[gmx-users] Percentage of H-bonds

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

Re: [gmx-users] xpm 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

[gmx-users] xpm file

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

[gmx-users] trjconv -pbc

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

[gmx-users] Protein out of the box (not PBC problem)

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

Re: [gmx-users] incomplete frame

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

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

[gmx-users] incomplete frame

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

[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

[gmx-users] Dimer 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

Re: [gmx-users] Dimer g_rms

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

[gmx-users] g_anaeig -proj

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

[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] xpm file

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

Re: [gmx-users] g_rmsf -res

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

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

[gmx-users] g_rmsf -res

.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

[gmx-users] g_energy graph .xvg

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

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

[gmx-users] tpr file

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

[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

[gmx-users] Potential Energy problem

.* 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

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

[gmx-users] H-bonds

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

[gmx-users] Extending simulations

: 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

[gmx-users] gen_vel error

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

[gmx-users] g_rms warning

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

[gmx-users] pdb gro files

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

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

[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

[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

Re: [gmx-users] pbc whole

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

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

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

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

Re: [gmx-users] pbc whole

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

[gmx-users] Average structure -s

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

Re: [gmx-users] pbc whole

+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

Re: [gmx-users] Average structure -s

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

[gmx-users] pbc whole

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

[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

Re: [gmx-users] Structure deformation

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

[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

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

[gmx-users] Load imbalance

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 list

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

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

[gmx-users] Heating

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

[gmx-users] 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

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

[gmx-users] Density

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

[gmx-users] add heavy atoms

: 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

Re: [gmx-users] add heavy atoms

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

[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

[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

Re: [gmx-users] Re: converting proper dihedrals into ryckaert-bellemans

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

[gmx-users] converting proper dihedrals into ryckaert-bellemans

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

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

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

[gmx-users] large VCM(group rest)

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

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

[gmx-users] water molecule cannot be settled

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

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

[gmx-users] Protein Domain Motion

Hi Is it possible to simulate the Protein Domain Motion by MD ? Thank you Lin You can do a Coarse-Grained MD using Martini forcefield. You can see huge domain motions on your protein. Regards, Carla ___ gmx-users mailing listgmx-users@gromacs.org