[gmx-users] Re: Error during CNP simulation
Hi Chris My EM works just fine if I use a cubical box of water, so I'm baffled as to what's going wrong in this case. I tried the entire process again, this time removing position restraints. Let me describe my entire procedure on this occasion, once again: 1) I first assembled a bilayer of 128 DOPC lipids, in a box of dimension 7.5 x 7.5 x 7.5 nm3. 2) I then removed the water molecules, resized the box length by changing the bottom line of the coordinate file, and inserted a CNP to an appropriate location, about 7 nm above the bilayer. 3) Then, I performed an energy minimization, and the CNP did not move about. So far, so good. 4) I solvated the box with water using genbox, and then attempted an energy minimization (using steepest descents). This is where the problem arises. These are the coordinates from the input coordinate file, before the energy minimization: 129F16C01 1793 10.600 3.474 3.330 129F16C02 1794 10.438 3.758 3.294 129F16C03 1795 10.381 3.588 3.947 129F16C04 1796 10.795 3.703 3.387 129F16C05 1797 10.564 3.308 3.584 129F16C06 1798 10.289 3.506 3.415 129F16C07 1799 10.322 3.939 3.528 129F16C08 1800 10.655 3.430 3.872 129F16C09 1801 10.840 3.479 3.620 129F16C10 1802 10.641 3.958 3.453 129F16C11 1803 10.342 3.876 3.850 129F16C12 1804 10.610 3.991 3.756 129F16C13 1805 10.675 3.736 3.950 129F16C14 1806 10.307 3.397 3.721 129F16C15 1807 10.862 3.787 3.699 129F16C16 1808 10.172 3.686 3.649 And these are the coordinates from the output coordinate file, within just TEN steps of energy minimization: 4849F16C01 6513 1.015 0.049 5.350 4849F16C02 6514 1.294 -3.135 4.063 4849F16C03 6515 0.663 -1.872 3.948 4849F16C04 6516 1.521 -1.365 3.815 4849F16C05 6517 2.111 -0.464 4.030 4849F16C06 6518 0.546 -2.205 6.177 4849F16C07 6519 -0.418 -2.289 6.608 4849F16C08 6520 -0.301 -1.054 4.991 4849F16C09 6521 -0.154 -1.757 5.881 4849F16C10 6522 0.595 -0.223 5.592 4849F16C11 6523 1.450 -0.980 7.148 4849F16C12 6524 0.055 -1.027 5.487 4849F16C13 6525 0.020 -0.473 5.753 4849F16C14 6526 1.492 -0.255 4.474 4849F16C15 6527 0.926 -0.762 4.489 4849F16C16 6528 0.147 -2.022 3.748 I have no idea why this is happening- that the molecule could move so much seems ridiculous. Besides the em.mdp file, is something wrong with, for example, my method of resizing the box? Thanks! Bharath --original message-- Sorry Bharath, I simply can not believe that a macromolecule drifted 3 nm during energy minimization. What happened to the intervening solvent? I think that you have some problem with your technique here. Why did you use 120 constraints? Is this for bonds within the CNP? You need to do 2 things: a) figure out what is going wrong with your EM... what you describe seems impossible to me. b) simplify your system to debug the problem. So you get the same warnings about too many constraints if you omit the position restraints? Chris. -- 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] Holes in the solvent!
Dear Arman, I've noticed a similar effect where large voids appear in a solvent when running long nose-hoover NVT simulations. I have checked and it is not a pbc artefact. I found that if I turn the thermostat off the holes go away. I've also found that reducing the number of cores removes the holes. I am currently investigating this for a bug report I submitted ( http://redmine.gromacs.org/issues/1012 ) It would be helpful if you could let me know if your using a nose-hoover thermostat and if so have a look at what happens if you run the system on fewer cores, and what happens if you turn off the thermostat (and run nve) after the system has equilibrated. Thanks, Richard On 30/10/2012 05:46, "Arman Mahboubi Soufiani" wrote: > Dear Chris, > > Thank you for your directions. NaCl concentration in my system is 0.14 M > and I often visualize the whole system and can see the ions around the > system but not in crystal form! > Well, it sounds really strange to me! And I don't know if I proceed with > such a system, I get scientific results or not?! > I appreciate your further helps. > > Best Regards > > Arman > > On Tue, Oct 30, 2012 at 4:39 AM, Christopher Neale < > chris.ne...@mail.utoronto.ca> wrote: > >> In addition to the comments of Dallas Warren, which seems quite possible >> and should be checked, >> are you sure that you are seeing real holes and not just salt crystals >> that look like holes when you render only >> the waters with VMD? I have found that, at NaCL concentrations above 1 M, >> lipid bilayers catalyze the formation >> of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field >> for ions. These crystals looked a lot >> like vacuum holes to me until I visualized the salt. >> >> Chris. >> >> -- original message -- >> >> I am simulating a protein on a polymer surface for further adsorption free >> energy calculation. >> However, after performing the NVT run either for short or long durations I >> found out that couple of holes appear in the physiological saline solution >> (solvent)!!! >> Additionally, even proceeding with a long NPT run the holes are still >> present in the system. >> I would be thankful if you could direct me what could be source of such a >> strange outcome. >> >> Best Wishes >> >> Arman >> >> -- >> 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] Holes in the solvent!
Dear Richard, Thank you for your kind response. I'm glad that my problem is not a rare one. Actually, I apply the simplest V-rescale as the thermostat. I run my system on one core! However, I have not tried turning off the thermostat and run a micro-canonical instead. Well, I got an idea to implement. I am going to try NPTs at high temperatures and anneal the system in order to find out whether I can get rid of these large voids (holes) or not! Do you have any idea if this can work or not?! Looking forward to hearing from you. Best Wishes Arman On Tue, Oct 30, 2012 at 8:35 AM, Broadbent, Richard < richard.broadben...@imperial.ac.uk> wrote: > Dear Arman, > > I've noticed a similar effect where large voids appear in a solvent when > running long nose-hoover NVT simulations. I have checked and it is not a > pbc > artefact. > I found that if I turn the thermostat off the holes go away. I've also > found > that reducing the number of cores removes the holes. I am currently > investigating this for a bug report I submitted ( > http://redmine.gromacs.org/issues/1012 ) > > It would be helpful if you could let me know if your using a nose-hoover > thermostat and if so have a look at what happens if you run the system on > fewer cores, and what happens if you turn off the thermostat (and run nve) > after the system has equilibrated. > > Thanks, > > Richard > > > > On 30/10/2012 05:46, "Arman Mahboubi Soufiani" > wrote: > > > Dear Chris, > > > > Thank you for your directions. NaCl concentration in my system is 0.14 M > > and I often visualize the whole system and can see the ions around the > > system but not in crystal form! > > Well, it sounds really strange to me! And I don't know if I proceed with > > such a system, I get scientific results or not?! > > I appreciate your further helps. > > > > Best Regards > > > > Arman > > > > On Tue, Oct 30, 2012 at 4:39 AM, Christopher Neale < > > chris.ne...@mail.utoronto.ca> wrote: > > > >> In addition to the comments of Dallas Warren, which seems quite possible > >> and should be checked, > >> are you sure that you are seeing real holes and not just salt crystals > >> that look like holes when you render only > >> the waters with VMD? I have found that, at NaCL concentrations above 1 > M, > >> lipid bilayers catalyze the formation > >> of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field > >> for ions. These crystals looked a lot > >> like vacuum holes to me until I visualized the salt. > >> > >> Chris. > >> > >> -- original message -- > >> > >> I am simulating a protein on a polymer surface for further adsorption > free > >> energy calculation. > >> However, after performing the NVT run either for short or long > durations I > >> found out that couple of holes appear in the physiological saline > solution > >> (solvent)!!! > >> Additionally, even proceeding with a long NPT run the holes are still > >> present in the system. > >> I would be thankful if you could direct me what could be source of such > a > >> strange outcome. > >> > >> Best Wishes > >> > >> Arman > >> > >> -- > >> 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
[gmx-users] Biphasic Systems
Dear Gmx Users, I made a biphasic system with water and hexane following Justin tutorial (800 hexane molecules) ,after adding the peptides in water phase, the number of the hexane molecules were reduced and some of them were shifted to the other side of water molecules (not at the interface of oil-water). any comments on this? Cheers Davoud -- 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: Error during CNP simulation
On 10/30/12 3:28 AM, Bharath K. Srikanth wrote: Hi Chris My EM works just fine if I use a cubical box of water, so I'm baffled as to what's going wrong in this case. I tried the entire process again, this time removing position restraints. Let me describe my entire procedure on this occasion, once again: 1) I first assembled a bilayer of 128 DOPC lipids, in a box of dimension 7.5 x 7.5 x 7.5 nm3. 2) I then removed the water molecules, resized the box length by changing the bottom line of the coordinate file, and inserted a CNP to an appropriate location, about 7 nm above the bilayer. 3) Then, I performed an energy minimization, and the CNP did not move about. So far, so good. 4) I solvated the box with water using genbox, and then attempted an energy minimization (using steepest descents). This is where the problem arises. These are the coordinates from the input coordinate file, before the energy minimization: 129F16C01 1793 10.600 3.474 3.330 129F16C02 1794 10.438 3.758 3.294 129F16C03 1795 10.381 3.588 3.947 129F16C04 1796 10.795 3.703 3.387 129F16C05 1797 10.564 3.308 3.584 129F16C06 1798 10.289 3.506 3.415 129F16C07 1799 10.322 3.939 3.528 129F16C08 1800 10.655 3.430 3.872 129F16C09 1801 10.840 3.479 3.620 129F16C10 1802 10.641 3.958 3.453 129F16C11 1803 10.342 3.876 3.850 129F16C12 1804 10.610 3.991 3.756 129F16C13 1805 10.675 3.736 3.950 129F16C14 1806 10.307 3.397 3.721 129F16C15 1807 10.862 3.787 3.699 129F16C16 1808 10.172 3.686 3.649 And these are the coordinates from the output coordinate file, within just TEN steps of energy minimization: 4849F16C01 6513 1.015 0.049 5.350 4849F16C02 6514 1.294 -3.135 4.063 4849F16C03 6515 0.663 -1.872 3.948 4849F16C04 6516 1.521 -1.365 3.815 4849F16C05 6517 2.111 -0.464 4.030 4849F16C06 6518 0.546 -2.205 6.177 4849F16C07 6519 -0.418 -2.289 6.608 4849F16C08 6520 -0.301 -1.054 4.991 4849F16C09 6521 -0.154 -1.757 5.881 4849F16C10 6522 0.595 -0.223 5.592 4849F16C11 6523 1.450 -0.980 7.148 4849F16C12 6524 0.055 -1.027 5.487 4849F16C13 6525 0.020 -0.473 5.753 4849F16C14 6526 1.492 -0.255 4.474 4849F16C15 6527 0.926 -0.762 4.489 4849F16C16 6528 0.147 -2.022 3.748 I have no idea why this is happening- that the molecule could move so much seems ridiculous. Besides the em.mdp file, is something wrong with, for example, my method of resizing the box? Do not manually resize the box. Use editconf -box and -center as appropriate to place all your components within the unit cell. While it may appear from visualization that your molecules are where you want them to be, they are not. -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] Biphasic Systems
On 10/30/12 5:21 AM, Davoud Zare wrote: Dear Gmx Users, I made a biphasic system with water and hexane following Justin tutorial (800 hexane molecules) ,after adding the peptides in water phase, the number of the hexane molecules were reduced and some of them were shifted to the other side of water molecules (not at the interface of oil-water). any comments on this? What commands did you use to produce the system? If done properly, this should not have happened. Hexane molecules traversing the box is likely just a PBC effect, but that would only occur over the course of a simulation (not simple system construction) and should be transient. -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] martian thing
Dear gmx users, Something very weird is happening with a .gro file and I wonder if any user has ever experienced something similar... I am doing umbrella sampling simulation on a peptide with capped termini residues (ACE and NH2). As starting structure for the pulling simulations I used the last frame from a 150 ns simulation, in order to asses the stability of my system before the umbrella procedure. I did NVT and NPT equilibration, and then the MD run. Then I extracted the last frame of that 150 ns run and placed it into an appropriate box for the pulling, so I run again editconf, genbox and energy minimization. Then at the equilibration step the weird thing came: in the .gro file I have the ACE residues written as NH2 in one of the chains! The atom names remain as they have to according to the force field nomenclature (CH3, HH31, HH32, ...) for this ACE of this chain, but it is name as NH2!!! This is happening only in this .gro file at this step. Everything is fine in the first equilibrations, the MD run, the energy minimization in the newbox... It just shows up after this equilibration. I wonder if I may just change NH2 to ACE where it is to be or it has to be with something more complicated. -- 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] Error during CNP simulation
You show different atoms before and after minimization so this is not proof of movement. I often resize my box by changing the value at the end of the file and have never had any problem with it. Of course, you do need to be careful with this and everything you do. Chris. -- original message -- My EM works just fine if I use a cubical box of water, so I'm baffled as to what's going wrong in this case. I tried the entire process again, this time removing position restraints. Let me describe my entire procedure on this occasion, once again: 1) I first assembled a bilayer of 128 DOPC lipids, in a box of dimension 7.5 x 7.5 x 7.5 nm3. 2) I then removed the water molecules, resized the box length by changing the bottom line of the coordinate file, and inserted a CNP to an appropriate location, about 7 nm above the bilayer. 3) Then, I performed an energy minimization, and the CNP did not move about. So far, so good. 4) I solvated the box with water using genbox, and then attempted an energy minimization (using steepest descents). This is where the problem arises. These are the coordinates from the input coordinate file, before the energy minimization: 129F16C01 1793 10.600 3.474 3.330 129F16C02 1794 10.438 3.758 3.294 129F16C03 1795 10.381 3.588 3.947 129F16C04 1796 10.795 3.703 3.387 129F16C05 1797 10.564 3.308 3.584 129F16C06 1798 10.289 3.506 3.415 129F16C07 1799 10.322 3.939 3.528 129F16C08 1800 10.655 3.430 3.872 129F16C09 1801 10.840 3.479 3.620 129F16C10 1802 10.641 3.958 3.453 129F16C11 1803 10.342 3.876 3.850 129F16C12 1804 10.610 3.991 3.756 129F16C13 1805 10.675 3.736 3.950 129F16C14 1806 10.307 3.397 3.721 129F16C15 1807 10.862 3.787 3.699 129F16C16 1808 10.172 3.686 3.649 And these are the coordinates from the output coordinate file, within just TEN steps of energy minimization: 4849F16C01 6513 1.015 0.049 5.350 4849F16C02 6514 1.294 -3.135 4.063 4849F16C03 6515 0.663 -1.872 3.948 4849F16C04 6516 1.521 -1.365 3.815 4849F16C05 6517 2.111 -0.464 4.030 4849F16C06 6518 0.546 -2.205 6.177 4849F16C07 6519 -0.418 -2.289 6.608 4849F16C08 6520 -0.301 -1.054 4.991 4849F16C09 6521 -0.154 -1.757 5.881 4849F16C10 6522 0.595 -0.223 5.592 4849F16C11 6523 1.450 -0.980 7.148 4849F16C12 6524 0.055 -1.027 5.487 4849F16C13 6525 0.020 -0.473 5.753 4849F16C14 6526 1.492 -0.255 4.474 4849F16C15 6527 0.926 -0.762 4.489 4849F16C16 6528 0.147 -2.022 3.748 I have no idea why this is happening- that the molecule could move so much seems ridiculous. Besides the em.mdp file, is something wrong with, for example, my method of resizing the box? Thanks! Bharath -- 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] steered pulling code on ligand-receptor complex
Hello, everyone! I'm a new user in gromacs, and now I have to perform a steered pulling code on a ligand-receptor complex. The ligand is to be pulled away from the binding site of the receptor, and umbrella sampling will be used to gain the PMF (potential mean force) curve. Then binding energy of the ligand-receptor complex would be estimated. The receptor contains 303 residues. While the ligand is pulling away, the whole receptor is restrained by posres, 1000 in x, y and z axis. Since the receptor is so large and umbrella sampling needs so much calculations, a very long time will be taken to complete the work. Now I have my question, is there anyway to reduce the taken time? Such as keeping only residues near the binding site to respect the whole receptor? Thank you all 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] Holes in the solvent!
Dear Arman, I have never seen holes appear in my solvent when running on 12 cores or fewer, or when running with langevin coupling or NVE. Running at higher temperatures (700K-1000K) did remove the holes from my system however, the RDF's were inconsistent on varying core counts (peeks and troughs moving by Angstroms). Low core counts tended to yeild the same RDF as a well thermalised and equilibrated NVE run or a langevin simulation. I currently have simulations queing which will use v-rescale so I can't comment on that thermostat yet but if you are seeing this on 1 core I don't think it is the same issue I've been seeing. Sorry, Richard On 30/10/12 08:56, Arman Mahboubi Soufiani wrote: Dear Richard, Thank you for your kind response. I'm glad that my problem is not a rare one. Actually, I apply the simplest V-rescale as the thermostat. I run my system on one core! However, I have not tried turning off the thermostat and run a micro-canonical instead. Well, I got an idea to implement. I am going to try NPTs at high temperatures and anneal the system in order to find out whether I can get rid of these large voids (holes) or not! Do you have any idea if this can work or not?! Looking forward to hearing from you. Best Wishes Arman On Tue, Oct 30, 2012 at 8:35 AM, Broadbent, Richard < richard.broadben...@imperial.ac.uk> wrote: Dear Arman, I've noticed a similar effect where large voids appear in a solvent when running long nose-hoover NVT simulations. I have checked and it is not a pbc artefact. I found that if I turn the thermostat off the holes go away. I've also found that reducing the number of cores removes the holes. I am currently investigating this for a bug report I submitted ( http://redmine.gromacs.org/issues/1012 ) It would be helpful if you could let me know if your using a nose-hoover thermostat and if so have a look at what happens if you run the system on fewer cores, and what happens if you turn off the thermostat (and run nve) after the system has equilibrated. Thanks, Richard On 30/10/2012 05:46, "Arman Mahboubi Soufiani" wrote: Dear Chris, Thank you for your directions. NaCl concentration in my system is 0.14 M and I often visualize the whole system and can see the ions around the system but not in crystal form! Well, it sounds really strange to me! And I don't know if I proceed with such a system, I get scientific results or not?! I appreciate your further helps. Best Regards Arman On Tue, Oct 30, 2012 at 4:39 AM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: In addition to the comments of Dallas Warren, which seems quite possible and should be checked, are you sure that you are seeing real holes and not just salt crystals that look like holes when you render only the waters with VMD? I have found that, at NaCL concentrations above 1 M, lipid bilayers catalyze the formation of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field for ions. These crystals looked a lot like vacuum holes to me until I visualized the salt. Chris. -- original message -- I am simulating a protein on a polymer surface for further adsorption free energy calculation. However, after performing the NVT run either for short or long durations I found out that couple of holes appear in the physiological saline solution (solvent)!!! Additionally, even proceeding with a long NPT run the holes are still present in the system. I would be thankful if you could direct me what could be source of such a strange outcome. Best Wishes Arman -- 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
[gmx-users] Re: Re: Error during CNP simulation
That seemed to fix it. Thank you so much! Regards Bharath >Do not manually resize the box. Use editconf -box and -center as >appropriate to >place all your components within the unit cell. While it may appear from >visualization that your molecules are where you want them to be, they are >not. > >-Justin > >-- > > >Justin A. Lemkul, Ph.D. > >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
Fw: [gmx-users] hessian conversion
Hi Gmxers, has anyone ever converted the GROMACS hessian (in ps^(-2)) to CHARMM hessian (in KCal/mol), even considering the individual unit, GROMACS hessian numbers are far bigger than those in CHARMM? thanks, Yao -- -- 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] Error in npt run - box size/ triclinic skew factor
When trying to do an npt run, I get the fatal error: The X-size of the box (3.999511) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.00). I should mention, I'm brand new to using gromacs so any assistance is greatly appreciated. My nvt run was fine. I used the following mdp file: title = OPLS Lysozyme NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator 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= yes ; Restarting after NVT 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 = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 = Protein ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar refcoord_scaling= com ; scale center of mass of reference coordinates compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off Thanks in advance. -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-npt-run-box-size-triclinic-skew-factor-tp5002482.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
