Re: [gmx-users] How to produce the photodissociation in Gromacs?
On 20/09/2012 1:08 PM, Rajiv Gandhi wrote: Dear all, Why all people cut the protein ligand bond to produce the photodissociation? Because MM forcefields typically assume bonds do not break or form. Electronic degrees of freedom are not directly considered in the model. For instances, In myoglobin, To simulate photodissociation of the CO complex, the Fe–CO bond of the starting structure was cut before any calculation.Fe-C bond were cut and instantaneously switch the heme force field from 6-coordinated Fe to that of the 5-coordinated Fe. I want to understand how we can delete this bond between Fe-CO to induce the photodisssociation ? After we cut the bond what it can do during MD simulation ? If you know enough about such a system to parametrize the bonded and non-bonded systems, then in principle you could watch the process of dissociation after cleavage. But I can imagine spending 6 months to do that parameterization and still failing. A modelling approach that works nicely for simple first- and second-row elements not undergoing chemical reactions need not be extensible to either transition elements or reactions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] distance calculation
Thanks Mark. I was using the following command as I got it in the manual. g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg But I could not able to find the way how to specify the indices of the two desired atoms. ( suppose I want to plot the distance between atom no. 500 (protein backbone) and atom no. 879 (ligand atom) with respect to time) On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 20/09/2012 2:05 PM, tarak karmakar wrote: Thanks Justin. But in my case I want to plot the distance between one atom in the backbone of the protein and other atom present in the ligand. Then how can I specify these two atoms I need for plotting the distance between them. g_dist treats the system as a list of atoms, and is ignorant of details like molecules. So you just need to tell it which atoms via their indices. Mark On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/19/12 2:55 PM, tarak karmakar wrote: Dear All, I want to calculate the distance between the nitrogen atom present in the ligand and the H- attached to the backbone of the protein along a long trajectory. So can anyone suggest me how to consider these two atoms to calculate and plot the distance along with the time ? g_dist with appropriate index groups. -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 -- Tarak -- 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 produce the photodissociation in Gromacs?
Could you tell me what is the procedure to cut the bond to produce the photodissociation? On Thu, Sep 20, 2012 at 3:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 20/09/2012 1:08 PM, Rajiv Gandhi wrote: Dear all, Why all people cut the protein ligand bond to produce the photodissociation? Because MM forcefields typically assume bonds do not break or form. Electronic degrees of freedom are not directly considered in the model. For instances, In myoglobin, To simulate photodissociation of the CO complex, the Fe–CO bond of the starting structure was cut before any calculation.Fe-C bond were cut and instantaneously switch the heme force field from 6-coordinated Fe to that of the 5-coordinated Fe. I want to understand how we can delete this bond between Fe-CO to induce the photodisssociation ? After we cut the bond what it can do during MD simulation ? If you know enough about such a system to parametrize the bonded and non-bonded systems, then in principle you could watch the process of dissociation after cleavage. But I can imagine spending 6 months to do that parameterization and still failing. A modelling approach that works nicely for simple first- and second-row elements not undergoing chemical reactions need not be extensible to either transition elements or reactions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-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] Re: Water molecules cannot be settled: V-rescale is the cause
Justin Lemkul wrote So the initial equilibration was NPT? Yes. Justin Lemkul wrote Did you ever try simply running NVT with either Berendsen or V-rescale before applying any type of pressure coupling? No, I haven't, and I don't remember seeing that described in any work flow. Justin Lemkul wrote Immediate application of NPT is often unstable for a variety of reasons, not necessarily the temperature coupling algorithm. All right, that's useful information. But what I am doing here is ripped from a tutorial file, and modified as little as possible. I try not to change things that I do not yet understand. My source for the MDP files was the lysozyme tutorial shell script that accompanied GROMACS 3.3. If there are procedures in that tutorial that are obsolete, I guess I'm finding that out the hard way. Justin Lemkul wrote Anyone is welcome to contribute to the wiki; it is a community project, after all. I would also be interested to see if it can be demonstrated that NPT with V-rescale + Berendsen is unstable after an independent NVT simulation with either method. I may take the time to try that experiment later. I'll report back with any findings. Thanks for your help! -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-tp4999302p5001131.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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! * 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] distance calculation
On 20/09/2012 4:21 PM, tarak karmakar wrote: Thanks Mark. I was using the following command as I got it in the manual. g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg But I could not able to find the way how to specify the indices of the two desired atoms. ( suppose I want to plot the distance between atom no. 500 (protein backbone) and atom no. 879 (ligand atom) with respect to time) See manual 8.1 for discussion, and http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx for more. Mark On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 20/09/2012 2:05 PM, tarak karmakar wrote: Thanks Justin. But in my case I want to plot the distance between one atom in the backbone of the protein and other atom present in the ligand. Then how can I specify these two atoms I need for plotting the distance between them. g_dist treats the system as a list of atoms, and is ignorant of details like molecules. So you just need to tell it which atoms via their indices. Mark On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/19/12 2:55 PM, tarak karmakar wrote: Dear All, I want to calculate the distance between the nitrogen atom present in the ligand and the H- attached to the backbone of the protein along a long trajectory. So can anyone suggest me how to consider these two atoms to calculate and plot the distance along with the time ? g_dist with appropriate index groups. -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 -- 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] Re: Water molecules cannot be settled: V-rescale is the cause
On 20/09/2012 4:34 PM, Ladasky wrote: Justin Lemkul wrote So the initial equilibration was NPT? Yes. Justin Lemkul wrote Did you ever try simply running NVT with either Berendsen or V-rescale before applying any type of pressure coupling? No, I haven't, and I don't remember seeing that described in any work flow. Point 8 of http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation mentions it. Justin Lemkul wrote Immediate application of NPT is often unstable for a variety of reasons, not necessarily the temperature coupling algorithm. All right, that's useful information. But what I am doing here is ripped from a tutorial file, and modified as little as possible. I try not to change things that I do not yet understand. My source for the MDP files was the lysozyme tutorial shell script that accompanied GROMACS 3.3. If there are procedures in that tutorial that are obsolete, I guess I'm finding that out the hard way. Using any single source can lead to problems. Sometimes tutorials are deliberately stripped down to produce a numerical result in quick time, but not via a method that is useful for a real problem. Material gets dated and busy authors don't get paid for keeping them up to date, unfortunately. Doing all the tutorial material you can find, even if you think the topic irrelevant, will add do the general knowledge you need. Further clues can be found in methods reported in published work, particularly relevant if on systems similar to yours, or by people you can see are highly experienced with GROMACS because they've published results from using it for a while. Mark Justin Lemkul wrote Anyone is welcome to contribute to the wiki; it is a community project, after all. I would also be interested to see if it can be demonstrated that NPT with V-rescale + Berendsen is unstable after an independent NVT simulation with either method. I may take the time to try that experiment later. I'll report back with any findings. Thanks for your help! -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-tp4999302p5001131.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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! * 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] Re: v-rescale
Hi Peter, Thanks for your response. Rather than dragging this thread too far off-topic, I'll direct you back to my thread, where I have just posted additional details. I took a warning message from GROMACS a bit too literally and it caused me to use conditions that blew up my simulations. I am interested in your protocol for the typical equilibration. If this is in fact standardized, do you have a reference? It doesn't match up with anything in the tutorial files I have been using to run my own simulations. Admittedly, those files are from GROMACS 3.3, and the procedures may be a bit out of date. -- View this message in context: http://gromacs.5086.n6.nabble.com/v-rescale-tp5001066p5001136.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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! * 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] Re: v-rescale
On 2012-09-20 12:18:02AM -0700, Ladasky wrote: Hi Peter, Thanks for your response. Rather than dragging this thread too far off-topic, I'll direct you back to my thread, where I have just posted additional details. I took a warning message from GROMACS a bit too literally and it caused me to use conditions that blew up my simulations. I am interested in your protocol for the typical equilibration. If this is in fact standardized, do you have a reference? It doesn't match up with anything in the tutorial files I have been using to run my own simulations. Admittedly, those files are from GROMACS 3.3, and the procedures may be a bit out of date. Generally it's probably not a good idea to rely on tutorials designed around 3.3 when a google search for gromacs tutorial shows a series of 4.5.x tutorials written by Justin himself, with explanations of why certain steps are conducted. (also when certain features may be implemented differently, such as the introduction of the v-rescale thermostat). -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Re: Water molecules cannot be settled: V-rescale is the cause
On 20/09/2012 5:08 PM, Ladasky wrote: Mark Abraham wrote This all sounds much like an issue with the topology or starting configuration. And it is for that reason that, during my debugging process, I switched back from the chimeric protein structures that I was building myself to a standard PDB structure for which I had previously completed a 5-ns stable run. I wanted to eliminate any problems that the starting configuration might have caused. Fair enough, and good strategy to simplify while learning. Mark Abraham wrote I have seen systems where 0.5 fs without bond constraints was necessary to relax issues with the initial conformation, and using position restraints on (say) all heavy atoms would have made this impossible. I'll keep in mind that even 1.0 fs is sometimes not short enough, when working far from equilibrium. That being said, the fact that I saw almost the same water molecule misbehave at almost the same simulated time point, whether I used a 2.0 fs or a 1.0 fs time step, gave me the strong hint that my simulation was both reproducible -- and wrong. And thus, that my time step was probably not the critical factor. Every time you change the ensemble (i.e. .mdp settings), which includes beginning, the system is generally not in equilbrium and that can lead to forces that physically jar it. One prefers to choose the longest stable time step for a long simulation that remains in equilibrium, in order to be efficient with computing resources. It doesn't follow that the preparation should use that time step. Particularly if the forces are large when not in equilibrium, subsequent displacements are large and the simulation can fail immediately, or set up weird resonance effects (think Tacoma Narrows bridge) that break things later. The same water molecule having the problem suggests a local effect, rather than a system-wide effect. Thus the starting position and not the protocol might be to blame, although a gentler protocol can often overcome a poor starting position. In particular, an isolated water molecule placed by genbox in the middle of a protein can show these kinds of problems. For this kind of reason visualizing the results of computational procedures is always essential. Mark Abraham wrote Your protocol from July was also asking for trouble by generating velocities and moving straight into an NPT ensemble with position restraints. Starting with an NVT ensemble can be better idea, particularly if the volume is not quite right. If you read my reply to Justin, you will know that I'm not deliberately trying to skip any steps. I have made minimal modifications to the MDP files that were part of the GROMACS 3.3 lysozyme tutorial shell script. That protocol included a position-restrained solvent equilibration step, and I used it as-is. OK, but the authors probably knew that they'd set things up to have the right density for their system, so that NPT with PR would succeed without problems. Doing multiple equilibration phases for pedagogical reasons might have meant the users of the tutorial spent more time doing that and not focusing on whatever the tutorial's objective really was. If the point of the tutorial was not to discuss equilibration issues, it might not make a sound choice for a template. I'm not married to the need to go straight to NPT, or even to use position restraints during solvent equilibration. If the starting configuration of my protein of interest shifts while I'm making adjustments to the solvent, I don't mind. I'm trying to watch it fold, and the end point is far more important to me than the starting point. Then getting rid of PR entirely is plausible. Did Berendsen himself ever post to this mailing list? I remember coming across this signature line on some GROMACS-related post: Why do YOU use constraints? In my case, the answer is, because that's what my tutorial recommended. It's one of the quotes GROMACS tools print out as they exist, and presumably an in-joke from years past. Mark Now, WHY would I have switched from a Berendsen temperature-coupling algorithm to the V-rescale algorithm? Because of this cautionary note that I started receiving in GROMACS 4.5 when I started the position-restrained mdrun: NOTE 1 [file pr.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Mark Abraham wrote Your observations on one system are not enough to reach this conclusion. v-rescale is normally quite appropriate for equilibration. The above hint is one that only matters when you wish to perform proper equilibrium sampling. I understand that hint, in hindsight. It led me down a bit of a primrose path. Mark Abraham wrote Multiple phases of equilibration are normal, particularly in tricky cases, to gradually approach the conditions under which you wish to sample, via those that help deal with trouble with
Re: [gmx-users] distance calculation
thanks a lot Mark On Thu, Sep 20, 2012 at 12:31 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 20/09/2012 4:21 PM, tarak karmakar wrote: Thanks Mark. I was using the following command as I got it in the manual. g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg But I could not able to find the way how to specify the indices of the two desired atoms. ( suppose I want to plot the distance between atom no. 500 (protein backbone) and atom no. 879 (ligand atom) with respect to time) See manual 8.1 for discussion, and http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx for more. Mark On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 20/09/2012 2:05 PM, tarak karmakar wrote: Thanks Justin. But in my case I want to plot the distance between one atom in the backbone of the protein and other atom present in the ligand. Then how can I specify these two atoms I need for plotting the distance between them. g_dist treats the system as a list of atoms, and is ignorant of details like molecules. So you just need to tell it which atoms via their indices. Mark On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/19/12 2:55 PM, tarak karmakar wrote: Dear All, I want to calculate the distance between the nitrogen atom present in the ligand and the H- attached to the backbone of the protein along a long trajectory. So can anyone suggest me how to consider these two atoms to calculate and plot the distance along with the time ? g_dist with appropriate index groups. -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 -- 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 -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- 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] Some tips for decreasing CPU time for mdrun -rerun
Dear gmxers, I have generated MD simulation trajectory using gmx, and now I want to recalculate the energies and forces for the older trajectory by excluding interactions between two defined groups. Therefore, the older trajectory is used as one input option for mdrun through -rerun. In my opinions, the newer run shoud much quicker than the older one since only saved frames and less interactions are employed in this calculation. However, I find that the speed is almost same. How to decreasing CPU time for mdrun -rerun? I think I must have missed something. Could you please give me some hints? Thank you a lot for any reply. Yours sincerely, Chaofu Wu -- 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] specific dihedral plotting
On 20/09/2012 7:31 PM, tarak karmakar wrote: Dear All, I need to plot a specific dihedral in my protein and I have to see how it is changing with time. So while doing that I have created a new group for that specific dihedral by taking corresponding 4 atoms. Now, how could I specify this dihedral present in the index file while running g_dih program, as I see in the online manual options are as follows g_dih -f traj.xtc -s topol.tpr -o dih.out And it essentially gives the statistics of all the dihedrals. g_angle -type dihedral is probably more like what you want. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] Some tips for decreasing CPU time for mdrun -rerun
On 20/09/2012 7:26 PM, Wu Chaofu wrote: Dear gmxers, I have generated MD simulation trajectory using gmx, and now I want to recalculate the energies and forces for the older trajectory by excluding interactions between two defined groups. Therefore, the older trajectory is used as one input option for mdrun through -rerun. In my opinions, the newer run shoud much quicker than the older one since only saved frames and less interactions are employed in this calculation. However, I find that the speed is almost same. How to decreasing CPU time for mdrun -rerun? I think I must have missed something. Could you please give me some hints? Thank you a lot for mdrun -rerun requires neighbour searching for every frame of the trajectory, because it cannot assume spatial locality in the way that mdrun can. So it is possible for a rerun to do more work than the original. However in the absence of the timing breakdown reported at the end of the .log files, there's nothing much else to be said. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] problem pdb2gmx and acetylation
On 9/20/12 4:24 AM, menica dibenedetto wrote: Dear all, I have a problem with pdb2gmx function. I want to create the gro file of an acetylated at N-term protein. I copy here the head of the file: ATOM 2016 HC ACE 0 24.770 -62.381 -11.080 H ATOM 2015 CT ACE 0 25.644 -61.867 -10.739 C ATOM 2017 HC ACE 0 26.283 -61.657 -11.571 H ATOM 2018 HC ACE 0 26.167 -62.480 -10.034 H ATOM 2013 C ACE 0 25.231 -60.546 -10.063 C ATOM 2014 O ACE 0 24.058 -60.199 -9.966 O TER ATOM 2019 N MET 1 26.336 -59.728 -9.542 N ATOM 2020 H MET 1 27.236 -59.762 -9.976 H ATOM 1 CA MET 1 26.144 -59.704 -8.063 C The problem is that the output error told me that the atoms labels of ACE not correspond to the labels in the rtp file, but I checked it and them corresponds: Program pdb2gmx_d, VERSION 4.5.5 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom HC in residue ACE 0 was not found in rtp entry ACE with 6 atoms while sorting atoms. I used the amber99sb-ildn.ff What can I do? You've confused atom name with atom type. Refer to the aminoacids.rtp file for the force field. I would also suggest removing the TER from between the ACE and MET, otherwise pdb2gmx is likely going to try to write them as separate chains. -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
Re: [gmx-users] problem pdb2gmx and acetylation
Thanks!! :) now works! 2012/9/20 Justin Lemkul jalem...@vt.edu: On 9/20/12 4:24 AM, menica dibenedetto wrote: Dear all, I have a problem with pdb2gmx function. I want to create the gro file of an acetylated at N-term protein. I copy here the head of the file: ATOM 2016 HC ACE 0 24.770 -62.381 -11.080 H ATOM 2015 CT ACE 0 25.644 -61.867 -10.739 C ATOM 2017 HC ACE 0 26.283 -61.657 -11.571 H ATOM 2018 HC ACE 0 26.167 -62.480 -10.034 H ATOM 2013 C ACE 0 25.231 -60.546 -10.063 C ATOM 2014 O ACE 0 24.058 -60.199 -9.966 O TER ATOM 2019 N MET 1 26.336 -59.728 -9.542 N ATOM 2020 H MET 1 27.236 -59.762 -9.976 H ATOM 1 CA MET 1 26.144 -59.704 -8.063 C The problem is that the output error told me that the atoms labels of ACE not correspond to the labels in the rtp file, but I checked it and them corresponds: Program pdb2gmx_d, VERSION 4.5.5 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom HC in residue ACE 0 was not found in rtp entry ACE with 6 atoms while sorting atoms. I used the amber99sb-ildn.ff What can I do? You've confused atom name with atom type. Refer to the aminoacids.rtp file for the force field. I would also suggest removing the TER from between the ACE and MET, otherwise pdb2gmx is likely going to try to write them as separate chains. -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] How to create a box of molecules with three layer?
On 9/20/12 5:18 AM, Ali Alizadeh wrote: Dear All users How to create a box of molecules with three layer and a certain number of molecules? Use the logical of the biphasic systems tutorial as a basis: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html -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
Re: [gmx-users] specific dihedral plotting
Thanks Mark , I got it now :) On Thu, Sep 20, 2012 at 3:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 20/09/2012 7:31 PM, tarak karmakar wrote: Dear All, I need to plot a specific dihedral in my protein and I have to see how it is changing with time. So while doing that I have created a new group for that specific dihedral by taking corresponding 4 atoms. Now, how could I specify this dihedral present in the index file while running g_dih program, as I see in the online manual options are as follows g_dih -f traj.xtc -s topol.tpr -o dih.out And it essentially gives the statistics of all the dihedrals. g_angle -type dihedral is probably more like what you want. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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 -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- 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] Analysis of enssemble of MD trajectories
Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? 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] Analysis of enssemble of MD trajectories
On 9/20/12 6:06 AM, James Starlight wrote: Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? I think what you want is not concatenation, but rather simultaneous display. Analyze each trajectory separately and simply plot the data in one graph, i.e. 4 different RMSD traces in one panel. -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] Specifics on tabulated pair potentials
Hello! I am using gromacs for coarse grained systems. I have the need to represent breakable bonds. I have been using tabulated lennard-jones-cosine potentials with bonded interactions but now there is a need for proper non-bonded interactions on specific pairs. I have went through the manual but there seems to be very limited information on 'pair' interactions. Normally, I set my functypes to 8 or 9 for bonds, angles and dihedrals, and name the tables accordingly (table_b1.xvg etc.) I also have tabulated non-bonded interactions which I set up in the .mdp file. I have their tables with the appropriate names such as (table_S_P.xvg etc.). When I run mdrun with no special parameters, everything works nicely with all these things. I understand how I can add pair interactions in the topology file, but the function types are limited to 1 or 2, which I don't want to use. I want to use a tabulated potential. I understand that there is an option -tablep in mdrun, but I can't seem to understand how the whole thing works. So I want to have tabulated non-bonded interactions between specific pairs of (super)atoms. Is this possible and how should I go about doing that? Thanks in advance. I have been working on this project for a year, occasionally lurking on the mail list archives. This is the first mail I am sending. I truly appreciate the effort that is put into making and supporting this code. Cheers to you all. Murat -- 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] LINCS warning in md run
Hi, now I tried it without any restriction and still the LINCS warnings occur. Since it is always the hydrogen atom where the huge force lies on I had the idea just to remove the hydrogen atom to find out whether another atom will occur to have such a high force on or everything went fine. And indeed, without the hydrogen atom there is no problem during the MD run. Even when I fix all the other atoms. I can not see why this occurs. I already looked at the residue with pymol and I could see that there is no other residue or atom clashing with it. The residue looks like this: ATOM955 N TYP65 27.310 23.150 27.670 1.00 0.00 N ATOM956 CA TYP65 26.870 23.320 26.300 1.00 0.00 C ATOM957 C TYP65 27.920 23.760 25.300 1.00 0.00 C ATOM958 O TYP65 28.060 23.210 24.210 1.00 0.00 O ATOM959 CB TYP65 25.740 24.340 26.170 1.00 0.00 C ATOM960 CG TYP65 24.530 23.740 26.830 1.00 0.00 C ATOM961 CD1 TYP65 24.410 23.760 28.220 1.00 0.00 C ATOM962 CD2 TYP65 23.510 23.180 26.050 1.00 0.00 C ATOM963 CE1 TYP65 23.290 23.210 28.840 1.00 0.00 C ATOM964 CE2 TYP65 22.380 22.630 26.660 1.00 0.00 C ATOM965 CZ TYP65 22.260 22.630 28.070 1.00 0.00 C ATOM966 OH TYP65 21.160 22.100 28.670 1.00 0.00 O ATOM967 P TYP65 20.298 21.422 27.722 1.00 0.00 P ATOM968 OP1 TYP65 21.003 21.245 26.467 1.00 0.00 O ATOM969 OP2 TYP65 19.920 20.126 28.251 1.00 0.00 O ATOM970 OP3 TYP65 19.106 22.218 27.498 1.00 0.00 O ATOM971 H TYP65 27.210 23.914 28.325 1.00 0.00 H ATOM972 HA TYP65 26.485 22.366 25.933 1.00 0.00 H ATOM973 HB1 TYP65 25.524 24.543 25.119 1.00 0.00 H ATOM974 HB2 TYP65 26.010 25.270 26.669 1.00 0.00 H ATOM975 HD1 TYP65 25.154 24.234 28.821 1.00 0.00 H ATOM976 HD2 TYP65 23.603 23.156 24.973 1.00 0.00 H ATOM977 HE1 TYP65 23.200 23.222 29.916 1.00 0.00 H ATOM978 HE2 TYP65 21.603 22.189 26.053 1.00 0.00 H ATOM979 H1P TYP65 20.357 20.996 25.802 1.00 0.00 H The topology entry in the aminoacid.rtp file looks like this: [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 H1P OP1 [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB CE1 CE2CZOH The LINCS problems lie between the oxygen atom of the phosphate where a hydrogen atom is bound to (OP1) and the hydrogen atom bound to the oxygen atom of the phosphate (H1P). Do you see where the problem lies? Thank you, Eva On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Okey, now I tried it without any fixed residues. But still the energy after the minimization is not very low and I still get the LINCS warnings. The mdp file I use for the minimization looks like this: define = -DPOSRES Restraints during minimization generally restrict motion in the same way that freezing does. Again, this is a potential barrier to sufficient minimization. integrator = steep emtol = 10 nsteps = 1500 nstenergy = 1 energygrps
Re: [gmx-users] How to create a box of molecules with three layers?
On 9/20/12 6:54 AM, Ali Alizadeh wrote: Dear Justin I know ,I studied it, but it was two layer, I want to add three layer into my system! Right, you're not going to find an exact how-to for everything you might dream up. You can apply the same logic from the tutorial (creating independent solvent boxes and placing them in the same unit cell via manual positioning) to do what you want. -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] Re: gmx-users Digest, Vol 101, Issue 68
Dear Justin For example, In that tutorial(box vector : 3 , 3 , 10), At first, I add cyclo hexane into my system( center: 3 ,3 ,1) Then I add water with certain certain thickness(center: 3 , 3 , 5) Then I want to add cyclo hexane into my system( center: 3 ,3 , 8) Is it possible? How to? Sincerely -- 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] Analysis of enssemble of MD trajectories
Dear Dr. I might be wrong, but I think you can use g_rms with two seperate trj files, and it takes the rms from the starting structure of the first one. In which case you would have to decide which is the reference, and then just do it three times. Theres also auxiliarry software which has plugins for this, such as VMD, Pymol, or even O run in some sort of batch. In pymol I know it can be run as a script, but you need all saved pdb files extracted from each trj, so would be a bit large and pain. with the VMD it has plugins for them, but I only played with it once. If you only want to look at beginning and end rms from say the start and end for all traj-using just a couple pdb at either end would be easy in pymol and O. There is also these new tools I found in Bio R (its called Bio3D if you look on the web for the freeware) , which are all scripts that I tried once, which work as well, mostly the take a reference structure and parse the pdbs output from a trj (if you write out each individually) but there values are different but directtly correlatable (ie say 1.6 from the former and something like 80% is cranked out by the later Vs 0.4 and 5% meaning no change) Hope that helps, and if I am wrong about something somone corrects me. Stephan Watkins Original-Nachricht Datum: Thu, 20 Sep 2012 14:06:40 +0400 Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] Analysis of enssemble of MD trajectories Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? 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 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] LINCS warning in md run
On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, now I tried it without any restriction and still the LINCS warnings occur. Since it is always the hydrogen atom where the huge force lies on I had the idea just to remove the hydrogen atom to find out whether another atom will occur to have such a high force on or everything went fine. And indeed, without the hydrogen atom there is no problem during the MD run. Even when I fix all the other atoms. I can not see why this occurs. I already looked at the residue with pymol and I could see that there is no other residue or atom clashing with it. I suspect what is happening is that the topology is not stable. If removal of the H atom leads to stable trajectories, then it is experiencing some interaction that leads to the crash. Likely what is happening is that it is experiencing a very strong 1-4 interaction with the other phosphate oxygens and is being pulled very hard away from the oxygen to which it is bonded, leading to deformed geometry and the LINCS warnings. There are two possible solutions: 1. Modify the 1-4 interactions through an appropriate pair term. 2. Add exclusions to the topology between the H atom and each of the O atoms to which it is not bonded. I would recommend testing with a very simple system of TYP in water to validate that the topology is stable and rule out other factors. -Justin The residue looks like this: ATOM955 N TYP65 27.310 23.150 27.670 1.00 0.00 N ATOM956 CA TYP65 26.870 23.320 26.300 1.00 0.00 C ATOM957 C TYP65 27.920 23.760 25.300 1.00 0.00 C ATOM958 O TYP65 28.060 23.210 24.210 1.00 0.00 O ATOM959 CB TYP65 25.740 24.340 26.170 1.00 0.00 C ATOM960 CG TYP65 24.530 23.740 26.830 1.00 0.00 C ATOM961 CD1 TYP65 24.410 23.760 28.220 1.00 0.00 C ATOM962 CD2 TYP65 23.510 23.180 26.050 1.00 0.00 C ATOM963 CE1 TYP65 23.290 23.210 28.840 1.00 0.00 C ATOM964 CE2 TYP65 22.380 22.630 26.660 1.00 0.00 C ATOM965 CZ TYP65 22.260 22.630 28.070 1.00 0.00 C ATOM966 OH TYP65 21.160 22.100 28.670 1.00 0.00 O ATOM967 P TYP65 20.298 21.422 27.722 1.00 0.00 P ATOM968 OP1 TYP65 21.003 21.245 26.467 1.00 0.00 O ATOM969 OP2 TYP65 19.920 20.126 28.251 1.00 0.00 O ATOM970 OP3 TYP65 19.106 22.218 27.498 1.00 0.00 O ATOM971 H TYP65 27.210 23.914 28.325 1.00 0.00 H ATOM972 HA TYP65 26.485 22.366 25.933 1.00 0.00 H ATOM973 HB1 TYP65 25.524 24.543 25.119 1.00 0.00 H ATOM974 HB2 TYP65 26.010 25.270 26.669 1.00 0.00 H ATOM975 HD1 TYP65 25.154 24.234 28.821 1.00 0.00 H ATOM976 HD2 TYP65 23.603 23.156 24.973 1.00 0.00 H ATOM977 HE1 TYP65 23.200 23.222 29.916 1.00 0.00 H ATOM978 HE2 TYP65 21.603 22.189 26.053 1.00 0.00 H ATOM979 H1P TYP65 20.357 20.996 25.802 1.00 0.00 H The topology entry in the aminoacid.rtp file looks like this: [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 H1P OP1 [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2CGCB CE1 CE2CZOH The LINCS problems lie between the oxygen atom of the phosphate where a hydrogen atom is bound to (OP1)
Re: [gmx-users] How to create a box of molecules with three layers?
On 9/20/12 7:27 AM, Ali Alizadeh wrote: Dear Justin For example, In that tutorial(box vector : 3 , 3 , 10), At first, I add cyclo hexane into my system( center: 3 ,3 ,1) Then I add water with certain certain thickness(center: 3 , 3 , 5) Then I want to add cyclo hexane into my system( center: 3 ,3 , 8) Is it possible? How to? The logic for doing this is described explicitly in the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/02_construct.html -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
Re: [gmx-users] tutorial for liquid-solid simulation
On 9/20/12 7:55 AM, cuong nguyen wrote: Dear Gromacs Users, Could you please show me the tutorial for liquid-solid simulation? If it's not at http://www.gromacs.org/Documentation/Tutorials or found by Google, then it doesn't exist. -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
Re: [gmx-users] LINCS warning in md run
Hi Justin, thank you a lot for your answer. I will try it. Best, Eva On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi, now I tried it without any restriction and still the LINCS warnings occur. Since it is always the hydrogen atom where the huge force lies on I had the idea just to remove the hydrogen atom to find out whether another atom will occur to have such a high force on or everything went fine. And indeed, without the hydrogen atom there is no problem during the MD run. Even when I fix all the other atoms. I can not see why this occurs. I already looked at the residue with pymol and I could see that there is no other residue or atom clashing with it. I suspect what is happening is that the topology is not stable. If removal of the H atom leads to stable trajectories, then it is experiencing some interaction that leads to the crash. Likely what is happening is that it is experiencing a very strong 1-4 interaction with the other phosphate oxygens and is being pulled very hard away from the oxygen to which it is bonded, leading to deformed geometry and the LINCS warnings. There are two possible solutions: 1. Modify the 1-4 interactions through an appropriate pair term. 2. Add exclusions to the topology between the H atom and each of the O atoms to which it is not bonded. I would recommend testing with a very simple system of TYP in water to validate that the topology is stable and rule out other factors. -Justin The residue looks like this: ATOM955 N TYP65 27.310 23.150 27.670 1.00 0.00 N ATOM956 CA TYP65 26.870 23.320 26.300 1.00 0.00 C ATOM957 C TYP65 27.920 23.760 25.300 1.00 0.00 C ATOM958 O TYP65 28.060 23.210 24.210 1.00 0.00 O ATOM959 CB TYP65 25.740 24.340 26.170 1.00 0.00 C ATOM960 CG TYP65 24.530 23.740 26.830 1.00 0.00 C ATOM961 CD1 TYP65 24.410 23.760 28.220 1.00 0.00 C ATOM962 CD2 TYP65 23.510 23.180 26.050 1.00 0.00 C ATOM963 CE1 TYP65 23.290 23.210 28.840 1.00 0.00 C ATOM964 CE2 TYP65 22.380 22.630 26.660 1.00 0.00 C ATOM965 CZ TYP65 22.260 22.630 28.070 1.00 0.00 C ATOM966 OH TYP65 21.160 22.100 28.670 1.00 0.00 O ATOM967 P TYP65 20.298 21.422 27.722 1.00 0.00 P ATOM968 OP1 TYP65 21.003 21.245 26.467 1.00 0.00 O ATOM969 OP2 TYP65 19.920 20.126 28.251 1.00 0.00 O ATOM970 OP3 TYP65 19.106 22.218 27.498 1.00 0.00 O ATOM971 H TYP65 27.210 23.914 28.325 1.00 0.00 H ATOM972 HA TYP65 26.485 22.366 25.933 1.00 0.00 H ATOM973 HB1 TYP65 25.524 24.543 25.119 1.00 0.00 H ATOM974 HB2 TYP65 26.010 25.270 26.669 1.00 0.00 H ATOM975 HD1 TYP65 25.154 24.234 28.821 1.00 0.00 H ATOM976 HD2 TYP65 23.603 23.156 24.973 1.00 0.00 H ATOM977 HE1 TYP65 23.200 23.222 29.916 1.00 0.00 H ATOM978 HE2 TYP65 21.603 22.189 26.053 1.00 0.00 H ATOM979 H1P TYP65 20.357 20.996 25.802 1.00 0.00 H The topology entry in the aminoacid.rtp file looks like this: [ TYP ] [ atoms ] NN -0.5163001 CACT 0.2755032 HAH1 0.0082233 CBCT -0.3540524 HB1HC 0.1103265 HB2HC 0.1103266 CGCA 0.1197287 CD1CA -0.1989388 HD1HA 0.1371439 CE1CA -0.284884 10 HE1HA 0.177179 11 CZC0.452616 12 OHOS -0.534452 13 HH0.293600 14 CE2CA -0.284884 15 HE2HA 0.177179 16 CD2CA -0.198938 17 HD2HA 0.137143 18 CC0.536600 19 OO -0.581900 20 PP1.393213 21 OP1OH -0.752821 22 OP2O2 -0.822464 23 OP3O2 -0.822464 24 H1PHO 0.423316 25 [ bonds ] N H NCA CAHA CACB CA C CB HB1 CB HB2 CBCG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1CZ CZOS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 H1P OP1 [ impropers ] -CCA N H CA+N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1
Re: [gmx-users] hi
Hi, Welcome! :-) Sincerely, Shima From: marzieh dehghan dehghanmarz...@gmail.com To: gmx-users@gromacs.org Sent: Thursday, September 20, 2012 10:11 PM Subject: [gmx-users] hi -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problems in mdrun - CHARMM27
Hello Could you please take a look on my new pr.mdp file that I created for equilibrating water around lumiflavin. grompp works but I guess there must be something wrong because after grompp I am using mdrun and get this warning: Warning: 1-4 interaction between 1 and 5 at distance 2.429 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 1: Water molecule starting at atom 8655 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates My system is lumiflavin in a dodecahedron box, a tip3p water model and the CHARMM27 force field. This is my pr.mdp file: title = Lumiflavin NVT equilibration define = -DPOSRES ; Run parameters integrator = md nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = ISO SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed Thanks for helping me Best greetings Lara -- 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] Problems in mdrun - CHARMM27
On 9/20/12 3:04 PM, Lara Bunte wrote: Hello Could you please take a look on my new pr.mdp file that I created for equilibrating water around lumiflavin. grompp works but I guess there must be something wrong because after grompp I am using mdrun and get this warning: Warning: 1-4 interaction between 1 and 5 at distance 2.429 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 1: Water molecule starting at atom 8655 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates My system is lumiflavin in a dodecahedron box, a tip3p water model and the CHARMM27 force field. This is my pr.mdp file: You are not using correct settings. Peter posted these the other day for CHARMM27: http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html Beyond that, how successful was energy minimization? How did you derive the topology? Does an in vacuo run of just the solute work, or does it fail as well (implicates an incorrect topology)? -Justin title = Lumiflavin NVT equilibration define = -DPOSRES ; Run parameters integrator = md nsteps = 5; 2 * 5 = 100 ps dt = 0.002; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = ISO SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Thanks for helping me Best greetings Lara -- 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
Re: [gmx-users] Re: v-rescale
On 20/09/12 01:35, Peter C. Lai wrote: then switching to nose-hoover for production runs (as nose-hoover chains result in the correct canonical distribution)? I was under the impression that v-rescale resulted in the correct canonical distribution as well. Is this incorrect? -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] CHARMM27 Equilibrating Settings
Hello In my former questions I got some answers that leads me to following question (I am really thankful for that. This mailing list and the people here are great :-) ). I am using a CHARMM27 force field and it seems that I often used wrong settings in equilibrating and energy minimization. Some of this setting are told to me but I have now the questions: Where do I find this parameters for equilibrating and minimization for the CHARMM27 force field? I tried google and mostly I found my own questions here in this mailing list :( Thanks for help Greetings Lara -- 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] Re: v-rescale
On 20/09/2012 9:35 AM, Peter C. Lai wrote: I am not sure where the idea of using berendsen barostat with the v-rescale thermostat for equilibration came from, however. Doesn't the typical equilibration begin with v-rescale for temperature equilibration then adding parinello-rahman barostat then switching to nose-hoover for production runs (as nose-hoover chains result in the correct canonical distribution)? N-H does have known issues, see http://link.aip.org/link/doi/10.1063/1.2989802 and http://link.aip.org/link/doi/10.1063/1.2408420. I am not aware of any shortcomings of the Bussi v-rescale thermostat in GROMACS. Mark On 2012-09-19 04:24:27PM -0700, Ladasky wrote: Dear Sara, I just had a problem with my simulations that I traced to the use of the V-rescale temperature algorithm. Here is my recent post: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121 V-rescale may be appropriate in certain simulations, but it is apparently NOT appropriate when used with Berendsen pressure coupling during the initial equilibration. I don't know if that is related to your problem, but it's something that I just discovered the hard way. -- View this message in context: http://gromacs.5086.n6.nabble.com/v-rescale-tp5001066p5001122.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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! * 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] Re: v-rescale
I've done some extensive testing (paper on testing method in the works) and vrescale gives a very accurate ensemble very well for NVT. Parrinello-Rahman and MTTK are the only algorithms that are correct for NPT. Berendsen barostat is not. Note that there is a bug with vrescale + md-vv + that is fixed in 4.6 and (hopefully) for the next patch of 4.5. For equilibrating a system, Berendsen for both temperature and pressure is the best bet. They artificially minimize fluctuations, which is great for equilibration, bad for data collection. On Thu, Sep 20, 2012 at 6:05 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 20/09/2012 9:35 AM, Peter C. Lai wrote: I am not sure where the idea of using berendsen barostat with the v-rescale thermostat for equilibration came from, however. Doesn't the typical equilibration begin with v-rescale for temperature equilibration then adding parinello-rahman barostat then switching to nose-hoover for production runs (as nose-hoover chains result in the correct canonical distribution)? N-H does have known issues, see http://link.aip.org/link/doi/10.1063/1.2989802 and http://link.aip.org/link/doi/10.1063/1.2408420. I am not aware of any shortcomings of the Bussi v-rescale thermostat in GROMACS. Mark On 2012-09-19 04:24:27PM -0700, Ladasky wrote: Dear Sara, I just had a problem with my simulations that I traced to the use of the V-rescale temperature algorithm. Here is my recent post: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121 V-rescale may be appropriate in certain simulations, but it is apparently NOT appropriate when used with Berendsen pressure coupling during the initial equilibration. I don't know if that is related to your problem, but it's something that I just discovered the hard way. -- View this message in context: http://gromacs.5086.n6.nabble.com/v-rescale-tp5001066p5001122.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM27 Equilibrating Settings
Lara Bunte lara.bu...@yahoo.de wrote: Hello In my former questions I got some answers that leads me to following question (I am really thankful for that. This mailing list and the people here are great :-) ). I am using a CHARMM27 force field and it seems that I often used wrong settings in equilibrating and energy minimization. Some of this setting are told to me but I have now the questions: Where do I find this parameters for equilibrating and minimization for the CHARMM27 force field? I tried google and mostly I found my own questions here in this mailing list :( Thanks for help Greetings Lara -- 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 I have not found any rationale for changing the cutoffs during equilibration with charmm27. For some special cases (minimization in vacuum) I might increase/double the cutoffs just so each particle sees more neighbors due to the otherwise lower particle density. For MD runs (equilibration or production) I obtained my cutoffs from Roland Schulz at Oak Ridge National Laboratory: http://cmb.ornl.gov/members/z8g/cheat-sheet-for-gromacs) -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. -- 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] Input/output error in GROMACS
Dear all, I am trying to use editconf to produce a .GRO file from an .XYZ file but I am getting the following error: Program editconf, VERSION 4.0.5Source code file: futil.c, line: 330 File input/output error:S54NONSOLV.xyz.gro Some of the input file is:46S54 NONSOLVATED POLYMERC 5.33751 -1.90290 0.0C 5.75001-2.61740 0.0S 5.19791-3.23050 0.0C 4.44431-2.89490 0.0C 4.53051-2.07440 0.0C 3.01530-2.89490 0.0C 3.72980-3.30740 0.0C 3.72980-4.13240 0.0C 3.01530 -4.54491 0.0C 2.30080-4.13240 0.0C 2.30080-3.30740 0.0... The XYZ format is right. Is it that editconf cannot read .XYZ files although I understood otherwise.. Thanks Elie -- 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] Input/output error in GROMACS
On 9/20/12 8:00 PM, Elie M wrote: Dear all, I am trying to use editconf to produce a .GRO file from an .XYZ file but I am getting the following error: Program editconf, VERSION 4.0.5Source code file: futil.c, line: 330 File input/output error:S54NONSOLV.xyz.gro Some of the input file is:46S54 NONSOLVATED POLYMERC 5.33751 -1.90290 0.0C 5.75001-2.61740 0.0S 5.19791-3.23050 0.0C 4.44431-2.89490 0.0C 4.53051-2.07440 0.0C 3.01530-2.89490 0.0C 3.72980-3.30740 0.0C 3.72980-4.13240 0.0C 3.01530 -4.54491 0.0C 2.30080-4.13240 0.0C 2.30080-3.30740 0.0... The XYZ format is right. Is it that editconf cannot read .XYZ files although I understood otherwise.. A closer look at the code indicates that .xyz files are only read in certain circumstances, but I haven't looked closely. The fatal error indicates quite clearly that .xyz files are not accepted, since editconf appends a .gro extension to your file name. -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
Re: [gmx-users] Photodissociation through MD
On 9/20/12 9:35 PM, Rajiv Gandhi wrote: Dear all gromacs users, In myoglobin system, how we can cut the bond between Fe-C to produce the photodissociation through MD?. I have seen there are number of studies over photodissociation and also I believe that people have used their appropriate parameterization files to cut these bond. I am struct with this parameter and cutting bond process. It would be really appreciated if anyone can give some suggestion/information about this. Thanks a lot. Bonds cannot be broken or formed in classical MD. That process is more suited to QM/MM type calculations. Certainly the papers you have read provide methodology, and if you have specific questions on what has been done, it would likely be more efficient to contact the corresponding author(s) of those papers directly. -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
Re: [gmx-users] Photodissociation through MD
On 21/09/2012 11:35 AM, Rajiv Gandhi wrote: Dear all gromacs users, In myoglobin system, how we can cut the bond between Fe-C to produce the photodissociation through MD?. By not making it in your topology. Whatever procedure you follow for making the other Fe-C interactions needs to differ from the one you wish to model the cleaved bond. Mark I have seen there are number of studies over photodissociation and also I believe that people have used their appropriate parameterization files to cut these bond. I am struct with this parameter and cutting bond process. It would be really appreciated if anyone can give some suggestion/information about this. Thanks a lot. Sincerely Rajiv -- 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
