Re: [gmx-users] Resuming of the trajectory calculation
Very frequently it helps just to do some searches by your own and read _carefully_ the documentation: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend On 02/14/2013 08:13 AM, James Starlight wrote: Dear Gromacs Users! I have completed 100ns md trajectory. I 'd like to go on that simulation adding extra 100 ns to the existing trajectory (with appending of both trajectories in single file during that simulation) If I do it just via mdrun -v -cpi md -deffnm md the simulation have not gone on because the simulation time defined in mdp file was over. on contrary if I define new mdp file via grompt the second trajectory save in the another file Does it possible to continue simulation in the existing file? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Resuming of the trajectory calculation
It's all about comprehending reading. If you look carefully at the documentation again, you will find: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt What it's the right thing to do. On 02/14/2013 10:11 AM, James Starlight wrote: I've already tried to do it in accordance to that instructions! firstly I've created new tpr file where I changed only duration of my simulation grompp -f ./mdps/md_sd.mdp -n index -c old.tpr -o new.tpr then I've launched mdrun mdrun -v -s new.tpr -cpi old.cpi -deffnm old -append where old is the name of all files from old simulation. after this mdrun produced new set of all files and backuped (to the #old) previous files. But I want to extend simuklation in my existing files. James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Resuming of the trajectory calculation
Thank the documentation, which you should probably read more carefully the next time. Reading comprehension and discrete thinking are key. On 02/14/2013 10:59 AM, James Starlight wrote: Felipe, thats works perfect! thank you! James 2013/2/14 Felipe Pineda, PhD luis.pinedadecas...@lnu.se: It's all about comprehending reading. If you look carefully at the documentation again, you will find: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt What it's the right thing to do. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Run long-time MD process
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations On 01/21/2013 11:20 AM, Kieu Thu Nguyen wrote: Dear All, I intend to run a long-time MD process. Can i split it into many smaller processes without losing system properties ? Is that the following process will be followed from the results of the previous process ? Thank so much for any advice ! Regards, KT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] activation energy
I would first explain what do you mean with activation energy. What definition do you use? On 01/14/2013 01:15 PM, Ahmet yıldırım wrote: Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] activation energy
On 01/14/2013 01:29 PM, Ahmet yıldırım wrote: It is the minimum energy required to start a chemical reaction. OK. In a chemical reaction bonds are built or broken. None of this happens during a MD simulation. I have a structure complexed A and B ligands. I want to calculate how these ligands changed the activation energy. You would probably need some kind of (ab-initio) QM calculation to study this. It would be a better idea to ask, e.g., the Gaussian community (in CCL) for advice. 2013/1/14 Felipe Pineda, PhD luis.pinedadecas...@lnu.se I would first explain what do you mean with activation energy. What definition do you use? On 01/14/2013 01:15 PM, Ahmet yıldırım wrote: Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs demo
Maybe you can try first another tutorials, eg. http://manuals.bioinformatics.ucr.edu/home/linux-basics On 01/03/2013 03:16 PM, amna khan wrote: the command /usr/share/gromacs/tutor/gmxdemo/demo no such cooamnd found... cd /usr/share/gromacs/tutor/gmxdemo/demo permsion denied sudo /usr/share/gromacs/tutor/gmxdemo/demo comand not found i am not getting any results -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
Not to forget about the additional stochastic term in the V-rescale thermostat, when it's used. Since the equations are evidently deterministic, is the chaotic nature of MD just a numerical effect? The practical point: if the velocities are reset upon a restart from an equilibrated frame in order to generate multiple, independent trajectories for statistical purposes, the equilibration will be probably lost and a new equilibration phase will be needed. Is this correct? Best, Felipe On 11/22/2012 11:12 AM, Erik Marklund wrote: It will depend on the integration algorithms, parallelization, etc. The equations are deterministic, but numerical differences may arise e.g. from different ordering of floating point numbers being added together in different simulations. The chaotic nature of MD would then have the simulations diverge over time, but the question is how long it takes for such differences to really manifest. Best, Erik 22 nov 2012 kl. 10.13 skrev Felipe Pineda, PhD: Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Computational Chemistry and | | Biochemistry Laboratory | | School of Natural Sciences| | Linnaeus University | | SE-391 82 Kalmar | | Norrgård, room 311| | Sweden - Sverige | | Phone: ++46-480-44 6329 | | Mobile: ++46-76-8420572 | | E-Mail: luis.pinedadecas...@lnu.se| | Web:lnu.se| +---+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converting amber distributed parameters to gromacs.
ffamber.cnsm.csulb.edu/amb2gmx.pl On 11/07/2012 09:45 AM, Rajiv Gandhi wrote: Dear Gromacs user, I have found the parameters file for my ligand which is available in AMBER distribution parameter database, Could you advice me how do i use them in running over MD in gromacs? Thanks in advance, Regards Raju -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converting amber distributed parameters to gromacs.
There is not too much to say: the script is self-explanatory. Look also: http://www.gromacs.org/Documentation/Terminology/Force_Fields/AMBER?highlight=antechamber On 11/07/2012 10:27 AM, Rajiv Gandhi wrote: Could you please tell how do i use this script over amber file? Thanks. On Wed, Nov 7, 2012 at 5:58 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: ffamber.cnsm.csulb.edu/**amb2gmx.plhttp://ffamber.cnsm.csulb.edu/amb2gmx.pl On 11/07/2012 09:45 AM, Rajiv Gandhi wrote: Dear Gromacs user, I have found the parameters file for my ligand which is available in AMBER distribution parameter database, Could you advice me how do i use them in running over MD in gromacs? Thanks in advance, Regards Raju -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Computational Chemistry and | | Biochemistry Laboratory | | School of Natural Sciences| | Linnaeus University | | SE-391 82 Kalmar | | Norrgård, room 311| | Sweden - Sverige | | Phone: ++46-480-44 6329 | | Mobile: ++46-76-8420572 | | E-Mail: luis.pinedadecas...@lnu.se| | Web:lnu.se| +---+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of charged systems (2)
Hi, thanks to Justin for the pointer to the list archive I searched before with net charge, but without getting useful results. For the sake of clarity, I am not referring to the neutralizing plasma or neutralizing background charge used implicitly with PME, but to an additional net-charge correction implemented for example in CHARMM to avoid, at least partly, the artifacts produced by that neutralizing background charge in net-charged systems, which are sometimes unavoidable (s., eg., Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the ewald potential. Journal of Chemical Physics. 1998;108(17):7070-84. http://jcp.aip.org/jcpsa6/v108/i17/p7070_s1). Felipe On 11/05/2012 02:27 PM, Justin Lemkul wrote: On 11/5/12 8:16 AM, Felipe Pineda, PhD wrote: Hi again! many thanks to Xavier for his response, the only one I got so far ... I had the same impression, but I'm seeking for theoretically/technically more funded statements. My impression is also that there are different kind of equations depending of the treatment of long-range electrostatic interactions. My concrete question is now: are net charge corrections to the Ewald potential implemented in Gromacs? http://lists.gromacs.org/pipermail/gmx-users/2006-April/020821.html Searching the list archive for neutralizing background charge turns up a large number of results. This is a fairly common question, and there are many replies with varying degrees of detail. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of charged systems (2)
Hi again! many thanks to Xavier for his response, the only one I got so far ... I had the same impression, but I'm seeking for theoretically/technically more funded statements. My impression is also that there are different kind of equations depending of the treatment of long-range electrostatic interactions. My concrete question is now: are net charge corrections to the Ewald potential implemented in Gromacs? Thank you and kind regards, Felipe On 11/02/2012 10:54 AM, XAvier Periole wrote: From what I remember from my earlier impressions ... the equations are not correct when the system is not neutral. In your case the charge is significantly high ... On Nov 2, 2012, at 9:36 AM, Felipe Pineda, PhD wrote: Hi, I recently sent a query, but it was probably not appealing enough to get some feedback. So I try again with a shorter one: Is there any theoretical or technical objection against running an NPgammaT simulation on a charged (total charge = -36) membrane model (hydrated bipolar monolayer) using PME? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Simulation of charged systems
Dear Colleagues, I am currently carrying out MD simulations on models of archaeal membranes. These membranes, contrary to those of bacteria or eukariota, are made of unconventional lipids. In my case they contain a neutral carbohydrate headgroup and the second one is a negatively charged phospho-myoinositol, contrary to neutral (zwitterionic) phosphocholine found in conventional lipids. In order to have a neutral system to carry out the simulation on: 1. I could add 36 positive counterions (eg, Na+) to my membrane model, which would correspond to approx. 900 mM of these ions for the amount of water molecules I am using. This concentration is of course not only much higher than a physiological one, although it is, strictly speaking, not a salt, i.e. NaCl, concentration. The issue is that I would like to study the effect of salt (alkali cations) on the membrane properties and therefore would need a suitable, possible ion/salt-free system as reference state. 2. I could protonate the phosphate and have -O-P(OOH)-O- instead of -O-P(O2-)-O-. This would provide a neutral, salt-free reference state, but the issue is that this phosphate group would be probably de-protonated in the cellular compartment it is localized, which has a pH of approx 6. Another option would be to run the simulations on the charged system, without counterions, but I am not quite sure if there are technical problems with that. I am using the following settings for the treatment of long-range electrostatics: ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT I wonder if someone could kindly advise me in this issue. Any suggestion or comment will be highly appreciated. Best regards, Felipe +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Linnaeus University | | SE-391 82 Kalmar | | Sweden - Sverige | +---+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
To generate starting (non-equilibrated) bilayer structures for use in MD simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. Otherwise, for conventional lipids CHARMM-GUI membrane builder (http://www.charmm-gui.org/?doc=input/membrane). Hope it helps! Felipe On 10/04/2012 07:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
Hi, packmol generates just coordinates (pdb format) for optimized packing arrangements of whatever molecule you provide as input. It's up to you to parameterize the resulting model. CHARMM-GUI has a library of conventional (phospho)lipids and generates the input for CHARMM equilibration of the bilayer model built with those lipids. But, you should inspect by yourself the corresponding sites. Felipe On 10/04/2012 03:11 PM, James Starlight wrote: Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids. James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tau_t and tc_grps for v-rescale (2)
Hi again, I posted yesterday the query below, but have not received any feedback up to now. I would like to put my question in another way: in Justin's CAP-15 in DPPC tutorial he uses during NVT equilibration Bussi's thermostat (V-rescale) together with three separate coupling groups: ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K), Is this separate coupling needed at all taking into account that this temperature coupling method produces the correct coupling? Is it probably better to use a single coupling constant (system) and so avoid problems using this artificial correction to deal with the hot solvent / cold solute artifact? Could somebody kindly tell me how large could the coupling constant, tau_t, be? Is it OK to switch, e.g., from 0.1 to 0.3 ps after T equilibration is reached, i.e., during the production phase? Many thanks again in advance and kind regards, Felipe On 09/27/2012 03:49 PM, Felipe Pineda, PhD wrote: Hi, I'd greatly appreciate any general advice on the possibility to use several (2 or more) tc_grps with v-rescale and how large could be tau_t with this coupling method (is 0.3 ps still OK?). Many thanks in advance and best regards, Felipe -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tau_t and tc_grps for v-rescale
Hi, I'd greatly appreciate any general advice on the possibility to use several (2 or more) tc_grps with v-rescale and how large could be tau_t with this coupling method (is 0.3 ps still OK?). Many thanks in advance and best regards, Felipe -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding RMSD analysis result
It looks for me like the known pbc effect others already pointed to. If you have just a protein-ligand complex (+ water and counterions of course) it's relatively easy to manually (a piece of code would do it) bring the ligand to the correct position in the frames showing an abnormally high value by subtracting half the x/y dimension of the box from its coordinates and re-calculate the rmsd , but I think trjconv would do it as well. Felipe On 09/25/2012 09:22 AM, naga sundar wrote: Dear justin http://rmsdnagasundaram.blogspot.in/. This is the link to my rmsd graph. Plz check it once and suggest me. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding RMSD analysis result
On 09/25/2012 10:08 AM, naga sundar wrote: Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. Maybe because MD is stochastic ... As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. As Justin said, it's not about the pbc conditions as they appear in the mdp file, but about pbc effects due to a chain, probably the ligand, leaving the box and being reflected to the opposite side. Have you checked out visually how the weird frames look like? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Hi Sébastian, I think the magic word in this issue would be surface tension and the proper ensemble for the simulation NPgammaT. This is very well discussed in the paper I advised to you a couple of days ago. The issue is by no means trivial, although I'm not an expert to judge it. You can find an imho very well-founded theoretical discussion in, e.g., Lindahl, E. and Edholm, O. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J. Chem. Phys.(2000)113, 3882. Good luck! Felipe On 08/15/2012 08:23 PM, Sebastien Cote wrote: Thanks for the advices Chris. My peptide is known to be more favorably to PE than PC membrane that is why I am using POPE. Experimentally, the liquid phase transition is at 298K for POPE (if I am not mistaken). Is your 323K refer to some simulations? At first I wanted to use the new CHARMM36 lipids parameters because they are supposed to solve the previous CHARMM27 issue with the area per lipid. However, I am consistently obtained smaller APL then experiment and I am not able to reproduce the published APL obtained for POPE, even if I am starting from their equilibrated 80-POPE membrane and use same simulation conditions. That was the reason for starting this thread on the mailing list. Unfortunately, my peptide conformational space in solution is only well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as they do not have APL inconsistency and are united-atom. I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be made neglegible by using bigger membrane compared to my peptide's size (?). Sebastien From: chris.ne...@mail.utoronto.ca To: gmx-users@gromacs.org Date: Wed, 15 Aug 2012 17:29:29 + Subject: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? The area per lipid (APL) will certainly affect the free energy of peptide/protein binding to a lipid bilayer. I have not used charmm lipids extensively, but from what I understand they older charmm lipids required NPAT to get the correct APL. The newer charmm lipids were supposed to solve that problem, but I have heard it said that, though the problem has been alleviated to some extend, it still remains. If I were you, I'd use POPC in place of POPE. POPE is notorious for giving too-small APL's in simulations and I think it even requires temperatures of 323 K to enter the liquid phase. That said, I don't have a specific answer to your question of whether there are other affects of NPAT vs. NPT. It is plausible that NPAT-based fluctuations could affect the pathway or the kinetics. PS: I was not referring to lipid rafts, but the separate diffusion of the upper and lower leaflets. Once the peptide is fully inserted, if it spans both leaflets, this will tend to reduce this leaflet-specific diffusion and would represent an entropic penalty for binding (not sure how large). Chris. Dear Peter, I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as in Klauda's paper). I will retry with a more solvated membrane. Would you have any thought on how the NPAT ensemble might affect peptide-membrane interactions like I am studying i.e. peptide is totally solvated, then adsorb, and finally may insert? The paper on peptide-membrane interaction like this usually use united-atom lipid in the NPT ensemble. Most of the work I have seen on Charmm membrane in the NPAT ensemble were for embedded membrane protein. Sorry, but I only have experience with large pre-embedded membrane proteins, and those are governed both by signal sequences and post-translational modification. Chris's last email on the subject might lead to the hypothesis that lipid raft translation as the leaflets slide past one another could be a contributing factor to adsorbption of your species. Thanks, Sebastien -- gmx-users mailing list gmx-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 posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- +---+ | Luis Felipe Pineda De Castro, PhD
Re: [gmx-users] Parrinello-Rahman with surface-tension coupling
Thanks for the advice, Mark! I did exactly this experiment with the same expectations before posting my query. I didn't get any complaint neither from grompp nor from mdrun, what doesn't necessarily mean that this combination is implemented. I just noticed that during equilibration results deteriorate, i.e., the normal pressure which already was close to the target value gets negative, and the surface tension increases significantly over the target value. This could of course be an effect of the different pressure coupling method used. Kind regards, Felipe On 08/14/2012 07:28 AM, Mark Abraham wrote: On 13/08/2012 7:21 PM, Felipe Pineda, PhD wrote: Dear All, the Gromacs User Manual V.4.5.4 states on p. 33: (...) the surface tension and the z-component of the pressure can be coupled to a pressure bath. Presently, this only works with the Berendsen pressure coupling algorithm in GROMACS. My question: does this hold for V. 4.5.5 as well? Is it possible to use the combination: pcoupl= Parrinello-Rahman pcoupltype = surface-tension in an mdp file for a NPgammaT MD run? Probably, but you should try it and see :-) Likely grompp will complain if it is not implemented. Mark -- 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 posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Hi Sébastien, I found the following paper very instructive about this issue (simulated areas per lipid in bilayers): Jensen, M. et al. Simulations of a membrane anchored peptide: structure, dynamics, and influence on bilayer properties. Biophys. J. (2004)86, 3556-75 Take maybe a look at it, if you haven't done it already. Regards, Felipe On 08/13/2012 11:12 PM, Peter C. Lai wrote: Oh something I didn't mention: for bond constraints I used h-bonds instead of all-bonds. This may or may not make a difference (although I switched to h-bonds based on the suggestion of some charmm/lipid thread on here from a couple of years ago). On 2012-08-09 12:34:19PM -0300, Sebastien Cote wrote: Dear Peter, Did you use any different simulation conditions for your POPC membrane? I tried many different ones for POPE, without never reproducing Klauda's results. I may try yours on my POPE membrane. In my simulations, I want to study peptide-membrane interactions. The peptide is not embedded in the membrane. It is initially completely solvated without any interactions with the membrane. Then, I want to look at its adsorption and degree of insertion in the membrane. For that system, I can not remove the CoM motion of the protein alone, otherwise it will not adsorb and insert in the membrane. I may try (as you suggested) to remove CoM of the bottom leaflet on one hand, and the peptide-upperleaflet on the other hand. My peptide is not very long (17 to 35 amino acids), so I believe that remove the CoM of the peptide-upperleaflet/bottomleaflet will not have any pernicious effect. What do you think? Thanks for the suggestion, Sébastien Date: Wed, 8 Aug 2012 20:19:56 -0500 From: p...@uab.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? Personally, I could remove the COM of each leaflet when equilibrating the bilayer by itself (and as a side note I am not experiencing a similar problem with POPC that you're having with POPE...). However, after the protein is embedded, I have gotten good results for my protein, which extends from the water through the entire membrane into more water, by using a whole System COM removal. The introduction of my particular embedded protein acts as a physical coupling between the water layers with the lipids (not to mention if I choose to model the lipid raft localization crosslink, it will have to happen anyway). If your protein doesn't extend fully past both layers of the membrane you may want to stick with just coupling a Membrane+Protein+1 layer of water or Membrane+Protein and Water separately (like in Justin's KALP15 tutorial). You will have to decide what you think is physically realistic based on the interaction between the water, membrane, and protein when the protein is embedded. (if your protein is assymetrically embedded you may even use the following COM groups: protein+involved leaflet, second leaflet, water). On 2012-08-09 09:38:01AM +1000, Mark Abraham wrote: On 9/08/2012 3:28 AM, Sebastien Cote wrote: Thanks for the suggestion. I tried it, but for my system the gain is not significant. I was aware that it is preferable to remove the centre-of-mass for each leaflet separately. However, in my tests, I removed the center-of-mass of the membrane because I intent to simulate peptide-membrane interactions. In such case, the center-of-mass of the protein-membrane system is usually removed. Is their any way to remove the CoM motion of each leaflet separately on one hand, and peptide-membrane system CoM motion on the other? See 7.3.3 of manual. Mark Thanks, Sebastien Date: Fri, 3 Aug 2012 11:10:22 -0400 Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? From: da...@cornell.edu To: gmx-users@gromacs.org Hello, I ran into similar issues for a DPPC bilayer. It might be possible that the two leaflets of the bilayer are moving with respect to eachother. If this is not taken into account, these artificial velocities will mean the simulation thinks it is at a higher temperature than it really is. If possible, you might want to try subtracting the center of mass motion of each leaflet, rather than the center of mass motion of the entire bilayer. This will allow the system to equillibrate to the correct (higher) temperature, and should increase the area per lipid of the bilayer. Hope this helps. -David On Thu, Aug 2, 2012 at 8:22 AM, Sebastien Cote sebastien.cot...@umontreal.ca wrote: Dear Gromacs users, I did new tests on the POPE membrane with CHARMM36 parameters, but I still always get area per lipid values that are smaller than experimental value by 4 to 6 Angstrom2. Here are my new tests. My initial configuration is an equilibrated POPE membrane with 80 lipids at 1 atm and 310K in NPT. It was taken from Klauda's website and it was obtained from the study in which the POPE parameters
[gmx-users] Parrinello-Rahman with surface-tension coupling
Dear All, the Gromacs User Manual V.4.5.4 states on p. 33: (...) the surface tension and the z-component of the pressure can be coupled to a pressure bath. Presently, this only works with the Berendsen pressure coupling algorithm in GROMACS. My question: does this hold for V. 4.5.5 as well? Is it possible to use the combination: pcoupl= Parrinello-Rahman pcoupltype = surface-tension in an mdp file for a NPgammaT MD run? Your help and comments will be greatly appreciated. Best regards, Felipe -- 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 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
