Re: [gmx-users] amber99sb_virtual site lipids dopc MCH3_N constraint types

On 27/03/2012 11:54 PM, Song Ke wrote: Dear All, I have a question about create and simulate dopc lipid virtual sites. I noticed in ffbonded.itp [ constrainttypes ] ; this section is implemented manually from bond& angle values ; constraints for rigid CH3 groups MCH3 CT 20.166426

Re: [gmx-users] dssp error

On 27/03/2012 8:50 PM, Albert wrote: hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your selected group trn version: GMX_trn_file (single precision) Reading fr

Re: [gmx-users] Calculating the electrostatic potential at a point over time

On 28/03/2012 12:13 PM, Andrew DeYoung wrote: Greetings, Is it possible to determine the electric potential at the location of an atom, relative to infinity? From physics, I think that electric potential (relative to infinity) at the position vector \vec{r} DUE TO a point charge q located at \v

Re: [gmx-users] Segmentation Fault using g_cluster

On 28/03/2012 1:00 PM, Davide Mercadante wrote: Dear Gromacs Users, I am trying to run g_cluster to find an average structure for my system and after giving the following command line: g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n --g g_cluster started without proble

Re: [gmx-users] Segmentation Fault using g_cluster

o use the code better. We just don't know yet. There's certainly room to improve the code. Mark Thank you again for the reply. It has been much appreciated. Davide From: Mark Abraham <mailto:mark.abra...@anu.edu.au>> Reply-To: Discussion list for GROMACS users <mailto:g

Re: [gmx-users] Position restraints problem

On 28/03/2012 6:52 PM, Jernej Zidar wrote: Hi. After successfully importing a CHARMM-generated PDB file to GROMACS I set out to do some short simulations. While all calculations finished without a problem if everything but the water molecules were fixed. Removing the position restraints le

Re: [gmx-users] Position restraints problem

On 28/03/2012 7:39 PM, Jernej Zidar wrote: On Wed, Mar 28, 2012 at 16:17, wrote: See the warning in genrestr -h. If all you're doing is adding a single atom of position restraint per moleculetype, you can do that by hand faster than using make_ndx and genrestr and adding the #include. Mark T

Re: [gmx-users] on MD at constant pH

On 28/03/2012 9:42 PM, Justin A. Lemkul wrote: Acoot Brett wrote: Dear All, Currently is it possible to run MD at a constant pH value? The concept of pH is not well defined in MD simulations. In normal MD, you can't transfer protons and you can't explicitly model the actual hydronium c

Re: [gmx-users] Generation of the Distance Restraints

ms? Rigid constraints are not useful for you, because your initital conditions are a long way from your target conditions. Any kind of harmonic potential has the same or worse issues than you already have. Mark Thank for help again, James 22 ? 2012 ?. 17:32 Mark Abraham mail

Re: [gmx-users] Generation of the Distance Restraints

On 29/03/2012 5:53 AM, James Starlight wrote: Mark, thanks for explanation again. 28 ? 2012 ?. 16:04 Mark Abraham mailto:mark.abra...@anu.edu.au>> ???: That can mean big restraint forces and tiny integration steps and lots of tweaking and praying.

[gmx-users] crazy temperatures

On 29/03/2012 9:39 AM, Asaf Farhi wrote: Dear GMCS users Hi. Does anyone know if MD at 2K is feasible? Please start new email threads rather than hijacking old ones. I doubt anybody knows the answer to your question. Force fields are parameterized to reproduce data at around 300K. I can

Re: [gmx-users] using MPI

On 29/03/2012 12:25 PM, cuong nguyen wrote: Thanks Erik, In case I run my simulations on 4 nodes, please let me know what do I have to add to the command to start "MPI"? I have used the commands: /grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top mdrun -s NVT_50ns -o NVT_50ns

Re: [gmx-users] Re:200 CPU, 3ns/day for 80,000 atoms

On 29/03/2012 11:03 AM, Dr. Vitaly V. Chaban wrote: I am using gromacs for membrane simulation (under CHARMM36 FF) which contains around 80,000 atoms. I've submitted over 200 CPU in the cluster for such system with 2 fs time step. And what really astonished is that the efficiency for such simul

Re: [gmx-users] About movie in GROMACS

On 29/03/2012 4:15 PM, rama david wrote: HI Gromacs Friends, I complete one simulation for 4 different molecule placed apart in box of dimension 4 4 4 .. when I used the trajectory I saw the one molecule interact with each other but they are getting broken because of box..(Some

Re: [gmx-users] Pressure coupling doubt

On 29/03/2012 5:38 PM, bipin singh wrote: Hello, I have two doubts regarding pressure coupling in Gromacs: 1) When I use pcoupl=no the mdp.out shows the following ; Pressure coupling pcoupl = no Pcoupltype = Isotropic nstpcouple = -1 ; Time consta

Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs

On 29/03/2012 4:53 PM, ros...@kth.se wrote: Shima Arasteh wants to a share a link on the Gromacs wiki: http://www.gromacs.org/ Shima Arasteh says: Dear Gromacs friends, I am a new user of Gromacs, following the kalp-15 in DPPC tutorial instruction but I face a fatal error when I enter this com

Re: [gmx-users] about g_mindist....

On 29/03/2012 7:20 PM, rama david wrote: Hi everybody , I run simulation of 4 same molecule keep apart in box of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are 284 ) force field = gromacs96 53a6 COM (center of mass) infirmation of molecules system size :

Re: [gmx-users] mpirun

On 29/03/2012 8:09 PM, cuong nguyen wrote: Dear Gromacs Users, as in the manual, I tried to run the simulation on 4 processors and used the command as follow: /mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x NVT_50ns -e NVT_50ns -g NVT_50ns -v/ Then I got the error: /mpirun

Re: [gmx-users] Not able to continue with Equilibration

On 29/03/2012 8:22 PM, Hendry wrote: Hi, I am using Gromacs 4.5.4. After successful minimization by SD, I continued with equilibration step but I got the below errors. I tried many times with different parameters but the problem still persists. I have given errors and md parameters of equili

Re: [gmx-users] about g_mindist....

e the right way .. On Thu, Mar 29, 2012 at 2:02 PM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 29/03/2012 7:20 PM, rama david wrote: Hi everybody , I run simulation of 4 same molecule keep apart in box of 4 4 4 dimension ..( 71 atom i

Re: [gmx-users] Velocity autocorrelation

On 30/03/2012 2:42 AM, Ignacio Fernández Galván wrote: Dear all, I'm trying to estimate the correlation time for my system, for the purpose of selecting a number of uncorrelated configurations and setting a good value for nstxout. My systems are usually small molecules in molecular liquids (w

Re: [gmx-users] Not able to continue with Equilibration

On 30/03/2012 8:39 AM, francesca vitalini wrote: Thank you Justin for your answer. I'm trying to add the position restraints to my protein, but I have a problem. My topology is made of a chain repeated twice and if I want to build the position restraints through genrestr from a gro file, the nume

Re: [gmx-users] protein melting experiment by GROMACS

On 30/03/2012 12:11 PM, Acoot Brett wrote: Dear All, I remember before I have read a something on melting the protein from a predefined starting temperature to a predefined end temperature by MD, so that after the MD we can look at the whole process to see which part of the protein unfold earl

Re: [gmx-users] Re: do_dssp error

On 30/03/2012 10:28 PM, Erik Marklund wrote: And I replied "What's your dssp version? The most recent ones have different flags that are not yet supported by gromacs." ... and I asked whether you'd read and followed the advice in do_dssp -h. Asking for more help without appearing to have use

Re: [gmx-users] Editing of the existing system

On 30/03/2012 5:27 PM, James Starlight wrote: Dear Gromacs Users! I have some system wich consist of protein in membrane-mimicking layer surrounded by water. I want to modify my existing system by adding small peptide fragment to this system. I want to dock this peptide to the some part of m

Re: [gmx-users] Editing of the existing system

On 31/03/2012 1:00 AM, James Starlight wrote: Mark, Also I'd like to know some more about most correct parametrisation of such new edited system. My new system consist of two proteins ( one- wich was initially and the second small peptide wich I've docked to the first protein). So now I need

Re: [gmx-users] large scale simulation?

On 31/03/2012 8:29 AM, Peter C. Lai wrote: Yeah I usually average 21ns/day on a openmpi-over-qdr infiniband cluster using fewer than 300 nodes and with a 100K system with 60K TIPS3P (hydrogen LJ terms) waters (single precision gromacs, ffw3, and openmpi compiled with icc 10.0.3) On similar hard

Re: [gmx-users] index.ndx files

On 31/03/2012 10:39 AM, Eduardo Oliveira wrote: Hi, I'm trying to set up a configuration file to but i keep gettin an error after the grompp_d run. I'm using the command line as follows: grompp_d -f stpr.mdp -c sistema_boxwater.gro -p sistema.top -o sistema_stpr.tpr -n Text in bold correspo

[gmx-users] Re: large scale simulation?

On 31/03/2012 3:40 PM, Albert wrote: Hi guys: thank you very much for your kind comments. Probably the most effective way is to optimize PME balance as Mark mentioned. It seems that Mark's methods improved much much better for the speed. If possible, could Mark share your experience how d

Re: [gmx-users] help needed

On 31/03/2012 6:02 PM, oindrila das wrote: *SIMULATION OF LYSOZYME IN WATER USING GROMACS-4.0.5 * STEP: TO NEUTRALIZE THE +8 CHARGE WITH 8 CL- MOLECULES* COMMAND GIVEN : [root@localhost gromacs-4.0.5]# genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8*

Re: [gmx-users] Re: hkl harker sections

On 1/04/2012 12:12 AM, lloyd riggs wrote: Hello all, Does anyone know where to look to do a slice of my unit cell along sections (energies, forces etc...) or to just give a list of all atoms in the slice. Something like an h,k,l or x,y,z slice through a section. You can use g_select to cre

Re: [gmx-users] g_tune_pme error in blue gene

On 1/04/2012 4:50 AM, Albert wrote: Hello: I am trying to run g_tune_pme in blue gene with following script: # @ job_name = bm # @ class = kdm-large # @ account_no = G07-13 # @ error = gromacs.info # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 160:00:00 # @ notifi

Re: [gmx-users] g_tune_pme error in blue gene

On 1/04/2012 9:13 AM, Mark Abraham wrote: On 1/04/2012 4:50 AM, Albert wrote: Hello: I am trying to run g_tune_pme in blue gene with following script: # @ job_name = bm # @ class = kdm-large # @ account_no = G07-13 # @ error = gromacs.info # @ output = gromacs.out # @ environment = COPY_ALL

Re: [gmx-users] ifp file in Gromacs?

On 1/04/2012 1:41 PM, Eric Will wrote: Hi Can gromacs use gromos forcefield file *.ifp? If so, could you please help me how to use it. I cannot just add it to the topology files like adding itp files. I searched the mailing list with no luck... This is not a file format GROMACS knows about.

Re: [gmx-users] 2 chain protein itp file

On 1/04/2012 3:03 PM, Acoot Brett wrote: Dear All, According to the lysozyme model in the tutorial of *Justin Lemkul *in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html, I am runing a 2 chain protein complex MD, and the steps are exactly same as in that on-lin

Re: [gmx-users] Possible error in the gromacs calculation

On 1/04/2012 5:44 PM, Acoot Brett wrote: Dear All, For the GROMACS 4.5.5, after installation the test link is unavaliable, thus we cannot run the test. For the AMBER, after we install it and run the test, although we can pass most of the tests, we cannot pass all of the tests. For GROMACS, can

Re: [gmx-users] Possible error in the gromacs calculation

quilibrium distributions are normally very expensive to obtain. Also, different observables might require different methods for good agreement with experiment, so there is no general answer for how to do things right, unfortunately. Mark Cheers, Acoot *From:* Mark Abraham *To:* Discussion list f

Re: [gmx-users] mdrun -rerun

On 2/04/2012 10:10 AM, Juliette N. wrote: Hi all, I have an enquiry regarding calculation of heat of vaporization by estimating intermolecular nonbonded energies using mdrun rerun option. mdrun -rerun should break the total nonbonded energy coming from nonboded energy of (different molecules

Re: [gmx-users] pdb2gmx error

On 2/04/2012 10:19 AM, Acoot Brett wrote: Dear All, I just run a pdb2gmx of a protein, the error message is " Fatal error: Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 5." According to the sugestion I have tried

Re: [gmx-users] pdb2gmx error

t all. The fifth in the sequence, then. Perhaps with a terminal residue. After all, you haven't told us anything about what you're doing. Mark I am looking forward to getting your suggestion. Cheers, Acoot *From:* Mark Abraham *To:* Discussion list for GROMACS users *Sent:* Monda

Re: [gmx-users] mdrun -rerun

On 2/04/2012 11:16 AM, Juliette N. wrote: On 1 April 2012 20:17, Mark Abraham wrote: On 2/04/2012 10:10 AM, Juliette N. wrote: Hi all, I have an enquiry regarding calculation of heat of vaporization by estimating intermolecular nonbonded energies using mdrun rerun option. mdrun -rerun should

Re: [gmx-users] mdrun -rerun

y for the rerun code to get new configurations except by reading the input trajectory. Mark On 1 April 2012 20:17, Mark Abrahamwrote: On 2/04/2012 10:10 AM, Juliette N. wrote: Hi all, I have an enquiry regarding calculation of heat of vaporization by estimating intermolecular nonb

Re: [gmx-users] mdrun -rerun in parallel?

neighbour searching every configuration. Mark Best, -- Forwarded message -- From: Juliette N. Date: 1 April 2012 22:10 Subject: Re: [gmx-users] mdrun -rerun To: Discussion list for GROMACS users On 1 April 2012 22:07, Mark Abraham wrote: On 2/04/2012 12:05 PM, Juliett

Re: [gmx-users] Adding Born Radii for implicit solvent MD

On 2/04/2012 7:57 PM, german.erlenk...@pharmazie.uni-halle.de wrote: Dear Gromacs-Users, I want to do a MD with implicit solvent. During this I'll get the following erros. GB parameter(s) missing or negative for atom type 'ca' GB parameter(s) missing or negative

Re: [gmx-users] Problems with simulation on multi-nodes cluster

to do with the .mdp contents. Mark James 20 ? 2012 ?. 18:02 Mark Abraham mailto:mark.abra...@anu.edu.au>> ???: On 20/03/2012 10:35 PM, James Starlight wrote: Could someone tell me what tell the below error Getting Loaded... Readi

Re: [gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

On 03/04/12, Andrew DeYoung wrote: > Hi, > > Is it possible to compute the total electrostatic energy of an atom over > time? By "total," I mean including all of the terms (short range Coulomb, > 1-4 Coulomb, and Ewald), not just the short range Coulomb and 1-4 Coulomb. > > This question i

Re: [gmx-users] how to get a minimized structure pdb

On 03/04/12, balaji nagarajan wrote: > > > > > > > > > > Dear Users ! > > I have done a minimization for a tetrapeptide in a water box > > with conjugate gradient minimization of 1000 steps > > when I convert it to pdb as below > > > trjconv -f em.trr -o min.pdb -s em

Re: [gmx-users] Is the PME domain decomposition flexible in some hidden way?

On 3/04/2012 11:58 PM, Paolo Franz wrote: Hello! I am wondering if the domain decomposition chosen by the code, once the number of cpus dedicated to PME is chosen,can be overridden somehow. That is, if in some sort there exist a reciprocal space equivalent of "-dd" for the domain decomposition

Re: [gmx-users] Re: Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

On 4/04/2012 12:11 AM, Andrew DeYoung wrote: Greetings, Thank you so much, Mark! Do you know if it is possible to extract just the real-space part (not the reciprocal space part) of the Ewald summation? (By "Ewald summation," I mean either the standard Ewald summation or PME.) That's what Co

Re: [gmx-users] Parallel Computation of g_rdf

On 4/04/2012 3:00 PM, Size Zheng wrote: Dear All, I plan to use g_rdf to analyze my system which has thousands of molecules and> 1ms total simulation time. I tried this command on a small system first and found it was very time-consuming. I am just wondering if g_rdf can be executed parallel

Re: [gmx-users] the -extend function of the tpbconv command

On 4/04/2012 6:24 PM, Acoot Brett wrote: Hi Justin and All, The on-line document on "Extending Simulations" writes, "You might want to use the -append option of mdrun to append the new output to the old files. Note that this will on

Re: [gmx-users] do_dssp

On 4/04/2012 10:02 PM, Justin A. Lemkul wrote: Bernhard Knapp wrote: Hi I have some problems to get do_dssp running: I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I copied it to the correct location: "c

Re: [gmx-users] File editing - only one layer of water around a molecule

On 4/04/2012 7:27 PM, Lara Bunte wrote: Hello I have a question about editing a pdb file. I have a molecule in a box of water as a pdb file. I want to remove all water except of ONE layer around he molecule. How to do that? Do you know a software that is able to do that? Do you know how it

Re: [gmx-users] Further discussion: the -extend function of the tpbconv command

On 5/04/2012 1:58 PM, Acoot Brett wrote: Dear All, According to "http://www.gromacs.org/Documentation/How-tos/Extending_Simulations"; , the commands for extending MD are: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt But if you read "http://www

Re: [gmx-users] on a on-line command for

On 5/04/2012 2:07 PM, Acoot Brett wrote: Dear All, In http://www-personal.umich.edu/~amadi/fwspidr_tutor.pdf , there is a command *tpbconv -f *traj.trr *-s *topol.tpr *-e *ener.edr *-o *tpxout.tpr *--until *$VALUE But we know we never

Re: [gmx-users] Re: do_dssp

On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 > /dev/null 2> /dev/null I am using the DSSPold version. What could

Re: [gmx-users] Re: do_dssp

On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 5/0

Re: [gmx-users] Re: do_dssp

of DSSP. Mark // On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin

Re: [gmx-users] how to change the timestamp of a xtc file

On 05/04/12, lina wrote: > On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote: > > trjcat -settime or trjconv -t0 > > Thank you, a further question, a trjcat-ed xtc file, which timestamp like > > 0-5 0-2 0-5 0-3 ... > > Are there someway to update them all in the trjcated ones? I've n

Re: [gmx-users] Re: do_dssp

; > > > > I have already set the pat for dssp in .bashrc using export command , I > > > don't know why this error is there. Is it due to renaming dsspcmbi to > > > dssp ?? > > > > > > > > > You have now reported testing a command d

Re: [gmx-users] something about tpr file

On 05/04/12, lina wrote: > > Hi, > > suppose I lost original .tpr file, > > can I get tpr file from the .xtc file ? I mean from the .xtc or trr > file, not by re-run grompp to generate tpr file. > > No Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

Re: [gmx-users] how to change the timestamp of a xtc file

On 05/04/12, lina wrote: > On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham wrote: > > > > > > On 05/04/12, lina wrote: > > > > On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote: > >> trjcat -settime or trjconv -t0 > > > > Thank you, a fu

Re: [gmx-users] Monitoring of Salt bridges during simulation Run

On 05/04/12, James Starlight wrote: > Bharat, Peter thanks for advises > > I've checked g_saltbr but not found possible definition of the specified > regions ( this utility lacks -n index.ndx option). How I could ignore > contacts between solvent and protein ? Use trjconv -n and tpbconv

Re: [gmx-users] further discussion on the mdrun -append function

On 6/04/2012 1:41 PM, Acoot Brett wrote: Dear All, Frim mdrun -h, I got the following message: /-[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names/ Thus there is the possibility that the series xvg c

Re: [gmx-users] Re: job failed

On 6/04/2012 3:36 PM, Albert wrote: hello: thank you very much for your kind messages. I first did minimization, the NVP with gradually heating the system from 0-310K, and them NPT production: NVT.mpd--- define = -DPOSRES -DPOSRES_LIG constraints= hbonds integr

Re: [gmx-users] Different results from identical tpr after MD

On 6/04/2012 3:53 PM, bipin singh wrote: Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such r

Re: [gmx-users] the g_rms function after we trjcat the trajectory files before and after extension

On 6/04/2012 4:57 PM, Acoot Brett wrote: Dear All, Before and after extention we have 2 trajectorty files, and by trjcat we got we, then we can do the g_rms g_rms -s *.tpr -f *_noPBC.xtc -o rmsd.xvg -tu ns But here for the g_rms command I find no matter whether we use the *.tpr of the initiat

Re: [gmx-users] Atom N not found....

On 6/04/2012 8:27 PM, rama david wrote: Hi Gromacs Friends and Justin , Thank you for reply and suggestion. These is short part of my PDB . ATOM 1 1H ACE 1 0.000 0.000 0.000 ATOM 2 CH3 ACE 1 0.000 1.090 0.000 ATOM 3 2H ACE 1 1.028 1.4

Re: [gmx-users] Atom N not found....

On 6/04/2012 9:05 PM, Mark Abraham wrote: On 6/04/2012 8:27 PM, rama david wrote: Hi Gromacs Friends and Justin , Thank you for reply and suggestion. These is short part of my PDB . ATOM 1 1H ACE 1 0.000 0.000 0.000 ATOM 2 CH3 ACE 1 0.000 1.090 0.000

Re: [gmx-users] MD after equilibration phase

On 7/04/2012 12:15 AM, bipin singh wrote: When we mention gen_vel=no ;And provide pdb as input with no velocities As mentioned in the manual: "The velocities are set to zero when there are no velocities in the input structure file" Please elaborate what does this sentence mean. Each atom mu

Re: [gmx-users] MD after equilibration phase

On 7/04/2012 12:37 AM, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your comments. One more question. Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option in mdp and save the output(-c) of mdrun as pdb file instead of gro file. No. Velocities are only save

Re: [gmx-users] MPI installation

On 8/04/2012 12:41 PM, bharat gupta wrote: Hi, I am trying to enable mpi fro mdrun in an already installed gromacs-4.5.5. Using a freshly unpacked tarball will eliminate some sources of problems. Shouldn't be necessary, of course, but since nobody can warrant something hasn't been broken acc

Re: [gmx-users] MPI installation

ed an OpenMPI version that fails. So the installation guide continues to recommend only OpenMPI. But nobody reads that, of course :-) Mark On Mon, Apr 9, 2012 at 11:11 AM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 8/04/2012 12:41 PM, bharat gupta wrote: Hi,

Re: [gmx-users] Box generation for monoclinic crystal - regd

On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type

Re: [gmx-users] Re: Simulation in the high temperature conditions

On 9/04/2012 4:18 PM, James Starlight wrote: By the way I've completed equilibration phase of my system ( receptor in Ccl4-water membrane mimicking layer) in the hight temperature conditions. :) During 3ns I gradually increased temperature from 300 to 700k with posres applied on the Ccl4 C at

Re: [gmx-users] Re: Simulation in the high temperature conditions

On 9/04/2012 7:27 PM, James Starlight wrote: Mark, If you make your layer boundaries perpendicular to some axis then you can use position restraints on water oxygens that have non-zero force constants only with respect to that axis. Then relax the water position restraints before

Re: [gmx-users] .itp file for "Fe" atom..

On 10/04/2012 4:58 AM, Kamalesh Roy wrote: can anybody help me to make an .itp file for "Fe" I am trying to simulate the protein containing an Fe atom where it is needed. See examples in ions.itp for the force field you are using. Hope that you find parameters for Fe already exist for your f

Re: [gmx-users] Rerun error - the file has been replaced or its content has been changed

On 10/04/2012 4:50 AM, Steven Neumann wrote: Dear Gmx Users, I am running umbrella sampling on the cluster. The wall time is 72 hours so I have to rerun my simulation every time. After first 72 hours I rerun my simulation: pbsexec mpiexec mdrun -s umbrella0.tpr -cpi umbrella0.cpt -append -d

Re: [gmx-users] Rerun error - the file has been replaced or its content has been changed

n Mon, Apr 9, 2012 at 8:04 PM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 10/04/2012 4:50 AM, Steven Neumann wrote: Dear Gmx Users, I am running umbrella sampling on the cluster. The wall time is 72 hours so I have to rerun my simulation eve

Re: [gmx-users] on g_rms analysis

On 10/04/2012 4:59 PM, Acoot Brett wrote: Dear All, Suppose I have done a 5-ns production MD, I want to analysis the rmsd from 1 to 3 ns, will you please tell me the corresponding g_rms command? g_rms has options that allow you to select the start and finish time for the analysis. Look them u

Re: [gmx-users] protein folding / pbc

On 11/04/2012 1:24 AM, Shi, Huilin wrote: Hi All, I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure. I set up pbc with the starting structure which is compact. When defining the box we use editconf and set up the

Re: [gmx-users] Box generation for monoclinic crystal - regd

help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric

Re: [gmx-users] multiple dihedral function types - regd

On 11/04/2012 3:33 AM, ramesh cheerla wrote: Dear gromacs users, For one of my residues i have two types of dihedral functions, i.e C-C dihedrals are in periodic type and C-O dihedrals are in the Ryckaert-bellemans type, now i want to generate the topology f

Re: [gmx-users] Can gromacs handle reflective boundary condition ?

On 10/04/2012 11:50 PM, stjohn55 wrote: Dear, Can gromacs handle reflective boundary condition, in order to remove the periodicity of Z-axis ? No. Mark Do I need to take advantage of walls and Ewald ? Thanks so much!

Re: [gmx-users] regarding micelle and its analysis

On 11/04/2012 3:48 PM, priya thiyagarajan wrote: hello sir, i am studying about micelle formation of surfactants. i performed my run for 10ns.. when i visualize my final md pdb file i got around 2 to 3 micelles. my doubt is while performing analysis , g_gyrate giving a value of around 3nm..

Re: [gmx-users] Van der waals types

On 11/04/12, Chrisostomos Batistakis wrote: > > Dear all > > I am looking in the manual but I don't understand... > > When using vdw-type =cut-off in the .mdp file, is the LJ potential only > truncated in the cut-off distance rc, or is it also shifted in order to > avoid discontinuity when

Re: [gmx-users] Van der waals types

tion of truncation does not arise. Mark > > > On Wed, Apr 11, 2012 at 12:18 PM, Mark Abraham > wrote: > > > > > > > > > > On 11/04/12, Chrisostomos Batistakis wrote: > > > > > > > > Dear all > > > > >

Re: [gmx-users] Van der waals types

> VLJ=V(r)-V(rc) for r > > > Regards, Chrysostomos > > > On Wed, Apr 11, 2012 at 1:01 PM, Mark Abraham wrote: > > > > > > > > > > > > On 11/04/12, Chrisostomos Batistakis wrote: > > > > > > > Dear Mark > > &

Re: [gmx-users] File editing - only one layer of water around a molecule

around the molecule and remove the rest. In appendix I put one of this .pdb files that you can see what I mean. Thanks for help Greetings Lara -------- *Von:* Mark Abraham *An:* Lara Bunte *Gesendet:* 14:07 Mittwoch, 11.April 2

Re: [gmx-users] GROMACS (w. OpenMPI) fails to run with -np larger than 10

On 11/04/2012 11:03 PM, Seyyed Mohtadin Hashemi wrote: Hello, I have a very peculiar problem: I have a micro cluster with three nodes (18 cores total); the nodes are clones of each other and connected to a frontend via Ethernet. I am using Debian squeeze as the OS for all nodes. I have comp

Re: [gmx-users] Parallel run on multiple nodes

On 4/04/2012 7:14 PM, Huaichen(Bobby) Zhang wrote: Dear GROMACS users, I'm a new user of GROMACS. The command "mpirun -np 8 mdrun" is working well in a node with 8 processors. Maybe. Standard installation procedure is to suffix mdrun with _mpi so that you and everyone else can be really sure

Re: [gmx-users] Re: GROMACS (w. OpenMPI) fails to run with -np larger than 10

file; maybe you are out of quota?” problem is fixed, i needed to set the NFS to sync instead of async. Mark Abraham wrote On 11/04/2012 11:03 PM, Seyyed Mohtadin Hashemi wrote: Hello, I have a very peculiar problem: I have a micro cluster with three nodes (18 cores total); the nodes are clon

Re: [gmx-users] File editing - only one layer of water around a molecule

On 12/04/2012 3:24 AM, Justin A. Lemkul wrote: Lara Bunte wrote: Could you please give how g_select is used? Reading g_select -h might have led you to try g_select -select 'help' Is there a tutorial for that? g_select -select 'help all' The information contained therein is very extensi

Re: [gmx-users] mdrun segmentation fault

On 12/04/2012 3:30 PM, priya thiyagarajan wrote: hello sir, Thanks for your kind reply.. i am performing final md run for 60molecules .. after i submitted my job for 5ns, when i analyse the result my run is completed only for 314ps initially.. At this point, you should have looked at your .

Re: [gmx-users] Question on checkpoint files and restarts/continuity

On 13/04/2012 2:36 AM, J. Nathan Scott wrote: Hi all, I had a very quick question I couldn't find an exact answer for that I'm sure someone here can answer very easily. The Gromacs website says (http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File): "A .cpt file is produced by mdru

Re: [gmx-users] mdrun -rerun

kul wrote: Juliette N. wrote: On 1 April 2012 20:17, Mark Abraham wrote: On 2/04/2012 10:10 AM, Juliette N. wrote: Hi all, I have an enquiry regarding calculation of heat of vaporization by estimating intermolecular nonbonded energies using mdrun rerun option. mdrun -rerun should break the total nonbon

Re: [gmx-users] Tabulated potential segmentation fault

On 13/04/2012 2:48 AM, Laura Leay wrote: All, I'm trying to run a tabulated soft core potential with the form V = A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential after this. I've chosen the parameters of this equation to be the same for all atoms in my system (a polymer

Re: [gmx-users] distance restraints fails

On 13/04/2012 3:08 AM, Qinghua Liao wrote: Dear gmx users, I tried to apply distance restraints to my system, but I found that it failed because the distance between the restraints atoms in the last frame is bigger than what we want. Distance restraints aren't magic. There has to be an acces

Re: [gmx-users] File editing - only one layer of water around a molecule

u need to learn how to create a layer from a definition that suits you, because you'll probably have to vary that definition until you're happy with the outcome. Mark Thanks for help Greetings Lara -------- *Von:* Mark Abra

Re: [gmx-users] File editing - only one layer of water around a molecule

ully the use of single and double quotes. Mark Greetings Lara -------- *Von:* Mark Abraham *An:* Discussion list for GROMACS users *Gesendet:* 11:51 Freitag, 13.April 2012 *Betreff:* Re: [gmx-users] File editing - only one layer of water around a molecule On 13/04/2012 7:29 PM, Lara Bunte wrote

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