Re: [gmx-users] confusion about implicint solvent

/Support/Mailing_Lists -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.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

[gmx-users] confusion about implicint solvent

sa_surface_tension= 0.0054 ; Temperature coupling tcoupl= v-rescale tc_grps = System tau_t = 0.1 ref_t = 310 ; Velocity generation gen_vel= yes ld_seed= -1 thank you for the help. cheers Francesco -- Francesco Carbone PhD

Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher

Hi, just try to disable OpenMP threads, unsetting OMP_NUM_THREADS environment variable Francesco 2013/8/1 akk5r ak...@virginia.edu Hi All, I am trying to run a membrane protein simulation on Gromacs 4.6 using the Charmm 36 force field parameters. I found the following parameters

Re: [gmx-users] gpu cluster explanation

On Fri, 12 Jul 2013, at 03:41 PM, Richard Broadbent wrote: On 12/07/13 13:26, Francesco wrote: Hi all, I'm working with a 200K atoms system (protein + explicit water) and after a while using a cpu cluster I had to switch to a gpu cluster. I read both Acceleration and parallelization

[gmx-users] storage problem during a simulation

END LOG thank you for your help cheers, Fra -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: [gmx-users] storage problem during a simulation

the simulations are still running, they should end tomorrow afternoon. Fra On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote: What does gmxcheck have to say about your output files? On Jul 23, 2013 12:17 PM, Francesco frac...@myopera.com wrote: Hi all, This morning the gpu cluster

[gmx-users] gpu cluster explanation

5d03h42:15 (ns/day)(hour/ns) Performance:9.7012.474 END STATISTICS thank you very much for the help. cheers, Fra -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx

Re: [gmx-users] how to describe the change of channel in the MD

or closed cavitiies) and outputs informations. I successfully used these two software to characterize tunnels and cavities in a MD simulation. Francesco 2013/6/19 aixintiankong aixintiank...@126.com Dear, In the MD, I find that when the ligand keep in the active site , the channel

[gmx-users] fftw without SIMD

Is it a known issue or I did something wrong? Francesco -- 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

Re: [gmx-users] Re: REMD analysis

Hi to everybody, Bharat, maybe i didn't follow exactly the wole tale, but is it possible you are running xmgrace without the -nxy option? You are probably visualizing the data related the 1st replica several times! Francesco 2013/5/24 Mark Abraham mark.j.abra...@gmail.com On Fri, May 24, 2013

[gmx-users] mdrun and simulation time

/normal that with the increase of the ns (always splitted in 2ns and extended) the running time is bigger? thank you Fra -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] mdrun and simulation time

in the last 4. Fra On Mon, 13 May 2013, at 11:53 AM, Justin Lemkul wrote: On 5/13/13 6:41 AM, Francesco wrote: Good morning all, This morning I checked the output of a 8ns (4 x 2ns) of simulation and I noticed a strange behaviour: The fist two simulations (each 2ns) ended up correctly

Re: [gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

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 -- Francesco Carbone

Re: [gmx-users] Conceptual question about the computational scaling of MD

Hi Andrew, maybe it is true on single processor simulations. It is false for sure when we talk about multicpu simulations because in this case each cpu has comunicate with each other and the implementations of this step makes a huge difference between the different codes. Francesco 2013/5/11

Re: [gmx-users] equilibration of the simulated systems

yes. you can use g_energy to plot what you need (T, density or whatever) and decide if it is acceptable or not. In the latter case you simply have to extend your run (see http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) cheers Francesco On Tue, 7 May 2013, at 06:58 PM, Za

Re: [gmx-users] installation Gromacs-Fedora18

--disable-float for double precision and --enable-mpi if you need mpi remember that fftw and gromacs must have the same precision. hope this helps you cheers Francesco On Fri, 3 May 2013, at 09:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux

Re: [gmx-users] Problem with gromacs in Cluster

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 -- Francesco frac...@myopera.com -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] how to use the trjconv -sep and -skip to get the individual file

? Read http://www.gromacs.org/Support/Mailing_Lists -- Francesco frac...@myopera.com -- 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

Re: [gmx-users] trjcat set timestep/amb2gmx?

using as x the frame number. This could, at least, permitting to visualize the plot with xmgrace without postprocessing the .xvg Francesco 2013/4/16 Mark Abraham mark.j.abra...@gmail.com On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:23 PM, Steven Neumann

Re: [gmx-users] replica exchange data in cpt file

This is what I meant, in particular it is a problem when I want to analyze the data regarding the exchange probability. Francesco 2013/4/4 João Henriques joao.henriques.32...@gmail.com So let me see if I understood what Francesco said correctly. Restarting a REMD job after hitting the cluster

Re: [gmx-users] replica exchange data in cpt file

if your -append option is activated (the default is yes), maybe Demux.pl reads the exchanging from the .log taking into account the time in the log and so you don't need to do anything. But I don't know how Demux.pl works :( Francesco 2013/4/4 João Henriques joao.henriques.32...@gmail.com

Re: [gmx-users] .top file from .tpr and .xtc

), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem

Re: [gmx-users] .top file from .tpr and .xtc

are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran

Re: [gmx-users] .top file from .tpr and .xtc

is present in .xtc file. CYS2 is present .rtp file of G43a1 forcefeild probably to form interchain disulfide bond reading from specbond.dat. Am I right in generating such half disulfide bond topology. shahid On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri francesco.ot...@gmail.com wrote

[gmx-users] replica exchange data in cpt file

attempts and probabilities are not stored so in each .log the data restart from 0 like a new simulation. Have I done something wrong or is it a known (except to me) issue? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: [gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

Hi Chris, I don't know if thngs changed in gromacs 4.6.x, but I succesfully did what you are triying to do setting the two variable GMXLIB and GMXDATA at the same time. Francesco 2013/3/5 Christopher Neale chris.ne...@mail.utoronto.ca Hello, I have downloaded the charmm36.ff directory

Re: [gmx-users] clusterization in dihedral space

Thank you Mark and Justin, do you have any reference where this kind of clustering is explained? I mean, since i need a parameter representing the difference between two frames to build the matrix, what is the parameter I can use starting from the dihedrals? Francesco 2013/1/22 Mark Abraham

Re: [gmx-users] clusterization in dihedral space

Thank you, but I don't see how performing cluster analysis with g_angle Francesco 2013/1/21 Justin Lemkul jalem...@vt.edu On 1/21/13 1:54 PM, francesco oteri wrote: Dear gromacs users, I am trying to run dihedral space clustering with g_dih, but I found that it gives me a lot of error

Re: [gmx-users] Convert .psf to .top

file. Francesco 2012/12/26 Kieu Thu Nguyen kieuthu2...@gmail.com Dear All, Are there any method that can convert CHARMM PSF files to Gromacs topology files ? Thank for any help ! Best regards, KT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Re: gold-S simulation

potential whose parameters can directly derived by the armonic form. Morse potential doesn't allow the bond breaking but the overall effect is very close! I have to admit I never used but only read about Morse potential so I cannot do practic advices! Francesco 2012/12/17 Justin Lemkul jalem

Re: [gmx-users] gold-S simulation

. If the distance is stable around the equilibrium value you can say that the interaction is still present Francesco 2012/12/16 fatemeh ramezani fr_...@yahoo.com hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you. Fatemeh Ramezani

Re: [gmx-users] gold-S simulation

Hi fatemeh, I am looking for prameters like yours, where have you took the parameters for gold and gold-aminoacid inteaction? Francesco 2012/12/16 Peter C. Lai p...@uab.edu Where is the .itp file for the system? On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote: hi I'm

Re: [gmx-users] g_sas : Total surface area

Hi Kavya, Can you better describe your system? As Mark suggested, could you supply some number? Francesco 2012/12/12 Mark Abraham mark.j.abra...@gmail.com On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was calculating solvent accessible surface

Re: [gmx-users] Error with MARTINI depending by the box size

Tanks to all for your advices, I am going to check all the different aspect you suggested and I will report the results as soon as possible. Francesco 2012/12/11 Tsjerk Wassenaar tsje...@gmail.com Hi, Visualization is the key. If you check the structure right after genbox, you should

Re: [gmx-users] Error with MARTINI depending by the box size

), the problem has to be in the bulk water! Francesco 2012/12/10 Justin Lemkul jalem...@vt.edu On 12/10/12 3:48 PM, francesco oteri wrote: Dear gromacs users, I am facing a very tricky problem in building a stable topology. In particular I am trying to use MARTINI force-field and I noticed

Re: [gmx-users] Error with MARTINI depending by the box size

. Francesco 2012/12/10 Justin Lemkul jalem...@vt.edu On 12/10/12 5:15 PM, francesco oteri wrote: Actually, since I copied and pasted the mail, there is an imprecision. When I use 20nm as box side lenght I don't get any error, everything goes fine. I actually tested different size between

Re: [gmx-users] Error with MARTINI depending by the box size

For Justin, I need this water for one simple reason: less then 20nm doesn't workAs I said before 2012/12/10 francesco oteri francesco.ot...@gmail.com Hi Mark, you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to use 0.21. Since I still got errors with this procedure

Re: [gmx-users] top2psf with Amber99SB-ILDN

hi,it would be nice knowing the errors. Francesco 2012/11/22, Steven Neumann s.neuman...@gmail.com: Dear Gmx Users, Is it possible to convert topology produced by Gmx and convert it ont the psf file? I used Justin script but when I load pdb and psf in VMD then there are some errors. Would

Re: [gmx-users] top2psf with Amber99SB-ILDN

assigned to bond part. The script provided here: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/top2psf.pl works much better. Steven On Thu, Nov 22, 2012 at 12:50 PM, francesco oteri francesco.ot...@gmail.com wrote: hi,it would be nice knowing the errors. Francesco

Re: [gmx-users] Re: hydrophobic contacts

)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 -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users

Re: [gmx-users] Continuous mdrun vs step-by-step mdrun

/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- 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

Re: [gmx-users] PCA

Hi Tuba, I guess you have to create an index for each peptide and then extracting covariance matrix on each peptide using the new indexes. Francesco 2012/11/6 Tuba Kilinc tkil...@gmail.com hi all, i would like to apply PCA (principal component analysis) for my peptides that i simulated. i

Re: [gmx-users] Martini FF for Sec structure changes...

://dx.doi.org/10.1021/ct200876v Francesco 2012/10/10 XAvier Periole x.peri...@rug.nl Nope, but on other softwares. On Oct 10, 2012, at 2:50 PM, rama david wrote: Thank you for your reply, Are these Cg can be used in Gromacs. Thank you in advance. With best wishes and regards, Rama david

Re: [gmx-users] Interaction study for peptide-receptor..

Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco

Re: [gmx-users] Interaction study for peptide-receptor..

2012/10/4 rama david ramadavidgr...@gmail.com Hi francesco, Thank you For reply. I did docking but the result are not so impressive. What does it mean not so impressive? I mean, do you have experimental data and the comparison with docking doesn't agree with experiments? Have you generated

Re: [gmx-users] Regarding g_cluster process MPI enabled

Francesco 2012/10/2 R.Vidya Rajendran (10PHD013) vidya2...@vit.ac.in Dear Friends, Gromacs script such as g_cluster takes lot of time to complete in a single machine. Is their any way to give this job to a cluster machine like mdrun. Since mdrun is MPI enabled so I can easily execute it on cluster

Re: [gmx-users] why the output of g_saltbr is so large?

Hi, because g_saltbr calculates the data regarding any charge-charge interaction ( neg neg, neg pos, pos pos). Small problem: every atoms (C,H,S,P...) has a charge so the outputs contains the distances among al the n*(n-1)/2 atom couples Francesco 2012/9/21 Albert mailmd2...@gmail.com

Re: [gmx-users] Analysis of enssemble of MD trajectories

! * 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 -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Photodissociation through MD

Hi, could you try to use the Morse potential for this bond. As far as I know, the parameters can be directly obatined forml the armonic potential expression. Francesco 2012/9/21 Mark Abraham mark.abra...@anu.edu.au On 21/09/2012 11:35 AM, Rajiv Gandhi wrote: Dear all gromacs users

Re: [gmx-users] why the output of g_saltbr is so large?

by g_saltbr as part of a putative interaction. Francesco 2012/9/21 Albert mailmd2...@gmail.com On 09/21/2012 10:48 AM, francesco oteri wrote: Hi, because g_saltbr calculates the data regarding any charge-charge interaction ( neg neg, neg pos, pos pos). Small problem: every atoms (C,H,S,P...) has

[gmx-users] is NOASSEMBLYLOOPS broken?

/pipermail/gmx-developers/2012-March/005714.html ? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

Re: [gmx-users] 1replica/1cpu problem

make install-mdrun 2012/7/19 Mark Abraham mark.abra...@anu.edu.au: On 19/07/2012 12:32 AM, francesco oteri wrote: Dear gromacs users, I am trying to run a replica exchange simulation using the files you find in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz The 4 replicas have

[gmx-users] 1replica/1cpu problem

replicas, I need to run 1cpu/replica. Has someone any idea of the probem? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support

[gmx-users] CMAP and Free Energy

Dear gromacs developers, is there any plan to make the CMAP correction avalaible for Free Energy Calculations? Dr.Oteri Francesco -- 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] floating point exception in .xtc file

Hi Christopher, you can try to use the program gmx_rescue, by Marc Baaden to recovery your trajectory. Below there is the adderess: http://baaden.free.fr/soft/compchem.html Francesco 2012/6/9 Mark Abraham mark.abra...@anu.edu.au On 9/06/2012 7:27 AM, Christopher Neale wrote: Dear Users

Re: [gmx-users] Writing and compiling new analyses for gromacs

function used, the only help I found is the gromacs source code. There are functions to read/write topology, frames, odb/gro file and so on Francesco 2012/6/4 Peter C. Lai p...@uab.edu On 2012-06-04 05:23:10PM -0400, Justin A. Lemkul wrote: On 6/4/12 5:16 PM, Shay Teaching

Re: [gmx-users] hydration layers around protein

saluti, Dr.Oteri Francesco -- 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] multiple dihedral definition and free energy calculation

reference I can find where the conversion is easly explained? Thank you, Francesco -- 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

Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

Hi Dariush, I've checked but it seems there no parameters for my detergent. Actully there are parameters for the polar head and the lipidic tail, so it is worth trying to merge them to have the correct representation! Francesco 2012/5/21 Dariush Mohammadyani d.mohammady...@gmail.com Have you

Re: [gmx-users] constraints between protein ligand - metal chelation

You are right Peter 2012/5/21 Peter C. Lai p...@uab.edu This approach still requires the system to be parameterized as a single moleculetype, doesn't it? On 2012-05-20 04:42:26PM +0200, francesco oteri wrote: Hi, if you are able to define atom couples able to mantein the structure

Re: [gmx-users] constraints between protein ligand - metal chelation

you impose a bond between the two atoms having as eauilibrium distance 0.6nm and force strenght 1000J. Function 6 doesn't implie the generation of angles and dihedrals so it is the right choice to impose distance restraints Francesco 2012/5/20 R.S.K.Vijayan biovija...@gmail.com Many thanks

[gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

Dear gromacs users, does someone of you know whether parameters for the detergent dodecyl-beta-maltoside are avalaible in MARTINI forcefield? Thank you in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] charm in gromacs

as functiontype 2 other as functiontype 3, so there is not an unique bondedtypes definition covering both the definition. Did I any mistake or actually there is a problem in the script? Francesco 2012/5/18 Mark Abraham mark.abra...@anu.edu.au On 18/05/2012 2:52 AM, francesco oteri wrote

[gmx-users] Re: mixing Urey-Bradley and armonic in the same rtp file

Dear gromacs users, I think I solved the problem. I converted armonic angle potentials in the Urey-Bradley potentials using 0 as constant for the 1-3 bond potential. Is it right in your opinion? Francesco 2012/5/16 francesco oteri francesco.ot...@gmail.com Dear gromacs users, I am trying

Re: [gmx-users] Two [ dihedrals ] sections in topology

-- Cordiali saluti, Dr.Oteri Francesco -- 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

[gmx-users] charm in gromacs

multiple periodic function (funtion 9), is it? Francesco -- 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] mixing Urey-Bradley and armonic in the same rtp file

potential between atom 1 and 3 present Urey-Bradley as a bond with same strenght and force value? Francesco grompp10.log 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

[gmx-users] poor performance in Hemiltonian Replica Exchange

for each .tpr file) but still I observe the same performance slowdown. I guess the free energy impairs the efficient force calculation, but I dont understand why. Can someone explain me the two observations? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] a question about ensemble

the tempaerature fixed around a value and the same for pressure, so I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, in priciple, right. Maybe convergence speed changes, but in this case banchmark are quite useful very welcolme! best, Francesco best Albert -- gmx-users

Re: [gmx-users] a question about ensemble

2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering

Re: [gmx-users] Lamb-Protein

Hi Justin, I have free-energy = no in my .mdp file, but I still see this value in g_energy. It should be absent or always 1 while the values by g_energy are close to 1 but still fluctuating along the trajectory. So, can you explain me how the value is used by gromacs? Francesco 2012

Re: [gmx-users] how to extract trajectories into individual pdb file?

. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] how to extract trajectories into individual pdb file?

-fit 2012/5/3 Albert mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing listgmx-users

Re: [gmx-users] Making Disulfide Bonds

Hi James, usually people run a minimization using distance restrain on the two atoms in order to make them closer. Then the obtained cnfiguration is used to recalculate the topology. Francesco 2012/4/28 James Starlight jmsstarli...@gmail.com Dear Gromacs Users! I have a model of my protein

Re: [gmx-users] Making Disulfide Bonds

Hi James, usually I insert by hand a bond in the topology file between the two atoms and then I minimize. This bond doesn't cause the generataion of angles and dihedrals, butit is enough to make the atom closer. Francesco Il 28/04/2012 16:08, James Starlight ha scritto: .. and the main

Re: [gmx-users] Velocities in trjconv 4.5.5

Hi Ignacio, actually .cpt contains velocities and, to extract a .gro containing them, you can try to use editconf. Francesco Il giorno 23 aprile 2012 16:45, Ignacio Fernández Galván jel...@yahoo.comha scritto: --- On Mon, 23/4/12, Alex Marshall amars...@uwo.ca wrote: I'm pretty sure .cpt

[gmx-users] problem with hemiltonian replica exchange restarting

.mdp:init_lambda=1.00 Thank you for help Francesco -- 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

Re: [gmx-users] Best Force Field for a Membrane Protein

. Francesco Il giorno 19 aprile 2012 08:32, Anirban Ghosh reach.anirban.gh...@gmail.com ha scritto: Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM

Re: [gmx-users] Fe atom problems....in simulation

Hi, You have to had LJ parameters in ffnonbonded.itp file in the subfolder relative to your force-field Francesco Il giorno 16 aprile 2012 11:08, Kamalesh Roy roy.kamales...@gmail.com ha scritto: CAn any one siggest me how can I run simulation a protein containing Fe atom, I have changed

Re: [gmx-users] progressive imbalance in REMD

Hi Marc, actually I am running NVT REMD so particle density is more or less constant along differet replicas. Is there any way to test which term takes more to be carried out? Francesco Il 13/04/2012 18:02, Mark Abraham ha scritto: On 14/04/2012 1:46 AM, francesco oteri wrote: Dear

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

/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 -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx

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

the work easier! Francesco Il giorno 13 aprile 2012 11:38, francesco oteri francesco.ot...@gmail.comha scritto: Hi Lara, the simplest way is using vmd. Briefly, 1) load the pdb file in vmd. 2) create a representation using a string like: same residue as within 3. of protein. where

[gmx-users] progressive imbalance in REMD

6.32679738562 7.21887045416 8.1979219038 9.45466733702 10.9115133233 12.5899111781 15.0987095693 19.5630970337 Of course this problem impacts on overall performances. My questions are: 1) Is the progressive imbalance expected? 2) Is there any way to alleviate the problem? Francesco -- gmx-users

Re: [gmx-users] how pdb2gmx calculate the total charge of a protein

Dear Acoot, the error, I guess, is you assumed the histidines are positive while I think they are neutral. Since the His protonation state is hard to identify at ph7, Hystidines are usually neutral. Francesco Il 07/04/2012 09:42, Acoot Brett ha scritto: Dear All, I have a protein

[gmx-users] REMD equilibration

or only in the NVT? Thanks in advance, Francesco -- 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

Re: [gmx-users] REMD equilibration

I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Francesco Il giorno 23 marzo 2012 10:53, Kukol, Andreas a.ku...@herts.ac.uk ha scritto: Hi Francesco, It should be the same

Re: [gmx-users] problem in oplsaa ffbonded.itp

OK, but for some AMBER dihedral the same goal has been obtained using an X for i and l atoms, like: X FE SS X 9 0.000.0 4 Why the same approach wasn't used for OPLSAA? Il giorno 21 marzo 2012 11:35, Justin A. Lemkul jalem...@vt.edu ha scritto: francesco

[gmx-users] bond managment in grompp

, and I noticed that these bonds are no more present and only right bonds are present. So, I am wondering why the fake bonds are inserted in topol.top and how grompp detectes these bonds. Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] bond managment in grompp

signal them. If the phenomena is not yet known, I can give you the data I used to generate the .top and .tpr. Francesco Il giorno 21 marzo 2012 16:18, Mark Abraham mark.abra...@anu.edu.au ha scritto: On 22/03/2012 1:46 AM, francesco oteri wrote: Dear gromacs user, I noted a strange behavior

Re: [gmx-users] Structural features for LINCS application

Il 16/03/2012 01:38, Mark Abraham ha scritto: On 16/03/2012 6:02 AM, Francesco Oteri wrote: Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only

[gmx-users] Structural features for LINCS application

with virtual site without all-bonds options. Thank you, Francesco -- 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

Re: [gmx-users] Resources on simulation walls

Hi Andrew, at http://manual.gromacs.org/online/mdp_opt.html#nl the manual says: Without walls or with only one wall the system size is infinite in the z direction. Therefore pressure coupling or Ewald summation methods can not be used. These disadvantages do not apply when two walls are used

[gmx-users] Fwd: charm to gromacs

Actually I solved the problem, I did a mistake in the bond conversion. Actually I found the right formula: k_gromacs = k_charmm**418.4**2 rising form the conversion from angstrom to nanometer -- Messaggio inoltrato -- Da: francesco oteri francesco.ot...@gmail.com Date: 08

Re: [gmx-users] How to input multiple trr files?

the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] a request regarding pdb2gmx and specbond.dat

Hi, I agree it could be very useful. You can insert the bond hand-coding it in the topology, but you need also to generate angle and dihedral. This is very boring and error prone. Francesco Il giorno 08 marzo 2012 12:32, Ehud Schreiber schr...@compugen.co.il ha scritto: Hi

Re: [gmx-users] Read mdcrd from AMBER --- Error Message

to contain the complete path of the molfile vmd directory. In my case, for example: VMD_PLUGIN_PATH=/apps/vmd/1.9/**lib/vmd /plugins/LINUXAMD64/**molfile Francesco Il giorno 08 marzo 2012 17:40, a a pat...@hotmail.com ha scritto: Dear Sir/Madam, I learnt that we can use mdcrd from AMBER

[gmx-users] LINCS problem with EM and Virtual sites

always the same result. The files I have used to run the minimization can be downloaded from http://160.80.35.105/download/vsite.tgz Has anyone of you any idea? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Re: Gromacs analysis tools for Namd output

= /lib/x86_64-linux-gnu/libc.so.6 (0x7f6e4ef8f000) libz.so.1 = /lib/x86_64-linux-gnu/libz.so.1 (0x7f6e4ed77000) /lib64/ld-linux-x86-64.so.2 (0x7f6e50de2000) If you miss this library, try to instrall again gromacs including this library Francesco Il 07/02/2012 20:04

Re: [gmx-users] Using groups in the mdp file

Hi Ignacio, You can solve the problem creating an index file through make_ndx. In such a file you need a group called ACX. Then use the index.ndx in grompp. Francesco 2012/2/6, Ignacio Fernández Galván jel...@yahoo.com: Hi all, I have a system with a molecule called ACX plus water (molecules

[gmx-users] high forces

. but I am not able to mantain the simulation stability. I am wondering whether exists a tool to dissect the energetic contributions ( including bonded parameters ) permitting me to identify the problem giving rise the crash. Francesco -- gmx-users mailing listgmx-users@gromacs.org http

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