Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass itamar.k...@monash.edu wrote: HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for anyone who is helps here. On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote: Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers or by ruling out possibilities. It is actually useful information to know that Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others ... but when it seems like you don't want to provide the requested information my first inclination is to give up on trying to help. At this point, there are a few unanswered old questions and I have some new questions. 1. Can you reproduce this with a water box? The error is reproducible in a box of protein and water only. 2. Can you reproduce this with your protein in vacuum? The error is reproduced in vacuum. 3. If neither 2 or 3, then can you step slowly from one of these systems toward your final system and identify the point at which the lincs warnings arise? 4. Do you get the warnings without Ca also, or just with Ca? I am not sure what this mean. I get this warning mainly for N-H, but also for Ca-C, pairs of atoms 5. Can you reproduce this with the SD integrator? If you are really against trying this, then at least can you reproduce this with a single Berendsen temperature coupling group? When I use SD integrator, the simulations run fine. 6. Can you reproduce this without using the reaction field? Either with PME or a simple cutoff? Using PME the system is running just fine. 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where you start to see this warning? I can't tell, 'cause I jump from 4.0.7 to 4.5.4. Thanks for the help, Itamar Chris. -- original message -- Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different. It's important to rule out different variables to arrive at a solution, which I suspect is of interest to you. You also haven't addressed points #1 and #6 in Chris' message. -Justin Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000 LINCS, but this is usually a sign that something bad is going on in the system. OK. Chris suggested a number of other strategies that will help determine which aspect of 4.5.4 is behaving differently. How did those strategies work out? Mark Cheers, Itamar On 18/08/2011, at 12:03 PM, chris.neale at utoronto.ca wrote: OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the
Re: [gmx-users] g_hbond
On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: One question for Glycine it is easy to assess 3 possible hbonds which can create as hydrogen is only one atom as a side chain. How about other amino acids and their maximum hbonds they can create? Any OH or NH group is a donor, any lone pair is an acceptor (though obviously not modeled explicitly in MD). The ability of MD force fields to agree with reality in this respect is debatable, but should come close. -Justin Thank you Justin. Can you please clarify me something and tell me whether I am wrong. This is what I obtained from calulating hbonds between 10 ligands and Glycine. Each ligand serve 8 OH group (flavanoid) : *Reading file md.tpr, VERSION 4.5.4 (single precision) Specify 2 groups to analyze: Group 0 ( r_96) has 7 elements -* this is my Glycine - 7 atoms (side chain - Hydrogen) *Group 1 (LIG) has 510 elements-* these are 10 ligands, 51 atoms each, 8 OH group *Select a group: 0 1 Selected 0: 'r_96' Select a group: Selected 1: 'LIG' Checking for overlap in atoms between r_96 and LIG Calculating hydrogen bonds between r_96 (7 atoms) and LIG (510 atoms) Found 81 donors and 112 acceptors * ** *81 donors? It should be 80 when I have 10 ligands with 8 Oh group... Am I right?* *112 acceptors? 7 atoms of my Glycine x 12 possibilities?* ** *trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 11x11x11 grid, rcut=0.35 Last frame 2000 time 10.000 Average number of hbonds per timeframe 0.642 out of 4536 possible - that is understood = (112x81)/2* ** *So how many possibilities has Glycine in order to create hbond? Shall I choose just a side chain which is hydrogen?* ** *Steven* Steven On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann s.neuman...@gmail.commailto: s.neuman...@gmail.com** wrote: Thank you for clarification Justin!!! The Manual is not as clear as you :P Steven On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Hi Gromacs Users, I have calculated hydrogen bonds and collisions between my ligands and every single residue using g_hbond. Looking at the criteria adpoted by Gromacs I found impossible that number of hydrogen bonds were higher than number of collisions... And what is interesting in one of my residue I obtained result like this... All Hbonds with Glycine - 1872, All Collisions 704. Does anyone know how is it possible? I don't know how any of your numbers are possible (1872 H-bonds forming with a glycine?), or what you are defining as a collision and how you calculated it. Please provide the exact commands that you're using. If you're equating a contact (e.g. from g_mindist) with a collision, then realize that the default criteria for a contact are very different than the geometric criteria for a hydrogen bond. -Justin -- ==** __== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ http://vt.edu/ http://vt.edu/ | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem http://www.bevanlab.biochem/**.
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass itamar.k...@monash.edu wrote: HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for anyone who is helps here. On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote: Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers or by ruling out possibilities. It is actually useful information to know that Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others ... but when it seems like you don't want to provide the requested information my first inclination is to give up on trying to help. At this point, there are a few unanswered old questions and I have some new questions. 1. Can you reproduce this with a water box? The error is reproducible in a box of protein and water only. 2. Can you reproduce this with your protein in vacuum? The error is reproduced in vacuum. 3. If neither 2 or 3, then can you step slowly from one of these systems toward your final system and identify the point at which the lincs warnings arise? 4. Do you get the warnings without Ca also, or just with Ca? I am not sure what this mean. I get this warning mainly for N-H, but also for Ca-C, pairs of atoms 5. Can you reproduce this with the SD integrator? If you are really against trying this, then at least can you reproduce this with a single Berendsen temperature coupling group? When I use SD integrator, the simulations run fine. 6. Can you reproduce this without using the reaction field? Either with PME or a simple cutoff? Using PME the system is running just fine. 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where you start to see this warning? I can't tell, 'cause I jump from 4.0.7 to 4.5.4. Thanks for the help, Itamar Chris. -- original message -- Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different. It's important to rule out different variables to arrive at a solution, which I suspect is of interest to you. You also haven't addressed points #1 and #6 in Chris' message. -Justin Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that
Re: [gmx-users] g_hbond
On 1/09/2011 6:14 PM, Steven Neumann wrote: On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: One question for Glycine it is easy to assess 3 possible hbonds which can create as hydrogen is only one atom as a side chain. How about other amino acids and their maximum hbonds they can create? Any OH or NH group is a donor, any lone pair is an acceptor (though obviously not modeled explicitly in MD). The ability of MD force fields to agree with reality in this respect is debatable, but should come close. -Justin Thank you Justin. Can you please clarify me something and tell me whether I am wrong. This is what I obtained from calulating hbonds between 10 ligands and Glycine. Each ligand serve 8 OH group (flavanoid) : /*Reading file md.tpr, VERSION 4.5.4 (single precision) Specify 2 groups to analyze: Group 0 ( r_96) has 7 elements* -/ this is my Glycine - 7 atoms (side chain - Hydrogen) /*Group 1 (LIG) has 510 elements*-/ these are 10 ligands, 51 atoms each, 8 OH group /*Select a group: 0 1 Selected 0: 'r_96' Select a group: Selected 1: 'LIG' Checking for overlap in atoms between r_96 and LIG Calculating hydrogen bonds between r_96 (7 atoms) and LIG (510 atoms) Found 81 donors and 112 acceptors */ *//* /81 donors? It should be 80 when I have 10 ligands with 8 Oh group... Am I right?/ You are assuming g_hbond knows what you know - that only your ligand hydroxyls can do effective H-bonding. However, g_hbond can only look at the atom names of the groups you give it. Algorithms do what you say, not what you mean, unfortunately. 81 = 1*1 + 8*10, since NH from glycine is a donor. /112 acceptors? 7 atoms of my Glycine x 12 possibilities?/ Methylene atoms cannot accept hydrogen bonds! See g_hbond -h. N and O from glycine are acceptors. 112 = 2*1 + 11*10 Mark *//* /*trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Will do grid-seach on 11x11x11 grid, rcut=0.35 Last frame 2000 time 10.000 Average number of hbonds per timeframe 0.642 out of 4536 possible - *that is understood = (112x81)/2/ // /So how many possibilities has Glycine in order to create hbond? Shall I choose just a side chain which is hydrogen?/ // /Steven/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Itamar, Yes, it appears that the 4.5.x series is more sensitive, due to the pressure coupling at intervals rather than at every step. Unfortunately the way it is now tied in with calculations of energies and neighbour searching indeed means that having nstpcouple set at 1 results in low simulation speeds. I find that the best approach is to equilibrate the system using a scheme as suggested to allow the system to get used to every perturbation (TC turned on, PC turned on, PC applied at intervals). Especially for the last step, the system has to 'get used' to having the pressure adjusted every nth step. The same holds for the transition from 4.0.7 to 4.5.x; it's in a sense a slight change of regime, to which the system has to get used. You can extend the simulation for a short period using nstpcouple=1, and then push it up higher again. Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 10:32 AM, Itamar Kass itamar.k...@monash.edu wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass itamar.k...@monash.edu wrote: HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for anyone who is helps here. On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote: Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers or by ruling out possibilities. It is actually useful information to know that Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others ... but when it seems like you don't want to provide the requested information my first inclination is to give up on trying to help. At this point, there are a few unanswered old questions and I have some new questions. 1. Can you reproduce this with a water box? The error is reproducible in a box of protein and water only. 2. Can you reproduce this with your protein in vacuum? The error is reproduced in vacuum. 3. If neither 2 or 3, then can you step slowly from one of these systems toward your final system and identify the point at which the lincs warnings arise? 4. Do you get the warnings without Ca also, or just with Ca? I am not sure what this mean. I get this warning mainly for N-H, but also for Ca-C, pairs of atoms 5. Can you reproduce this with the SD integrator? If you are really against trying this, then at least can you reproduce this with a single Berendsen temperature coupling group? When I use SD integrator, the simulations run fine. 6. Can you reproduce this without using the reaction field? Either with PME or a simple cutoff? Using PME the system is running just fine. 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where you start to see this warning? I can't tell, 'cause I jump from 4.0.7 to 4.5.4. Thanks for the help, Itamar Chris. -- original message -- Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk -- 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: cannot inactivate fitting in g_rmsf - incomplete coordinates are written
Surprisingly I could get complete coordinates from g_covar v4.5.4 without fitting, without being prompted to choose a group for the least squares fit. However, g_covar is much slower than g_rmsf and I would avoid using it for the whole trajectory if I could. I don't expect o get an answer in my original question, but at least I realized that g_covar firstly calculates the average coordinates and saves them in a .pdb file and then proceeds to covariance matrix calculations. So if I can kill the program at that point and do my job faster than with g_rmsf ;) -- 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] GROMACS 4.5.4 keep crashing all the time
I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk -- 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] Non-zero total charge
Hi, My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zero total charge: System has non-zero total charge: 5.70e+01 Please let me how i can rectify the situation. Many thanks, Munishika-- 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] Non-zero total charge
Munishika Kalia wrote: Hi, My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zero total charge: System has non-zero total charge: 5.70e+01 Please let me how i can rectify the situation. You haven't provided your genion command line (for the future, please always provide the exact command you used), but I suspect I know what the problem is anyway. You added 6 CL- ions, right? You initially had a +63 charge (6.3e+1 = 6.3 x 10^1). Hence you still have an unsatisfied charge of +57. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Non-zero total charge
6.30e+01 = 63 -- original message -- My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zero total charge: System has non-zero total charge: 5.70e+01 Please let me how i can rectify the situation. Many thanks, Munishika -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110901/58ff645a/attachment.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem building a polymer using pdb2gmx ....
Hi All I'm building a polymer (heterodimer) using pdb2gmx tool. I have included in ffG53a6 the 4 building block I need (aminoacids.rtp in my own dir: ../my_ffG53a6..): X ... A-B-A-B-A-B-A-B-A-B-A ... Y X: starting CAP residue A: a monomer B: the other monomer Y: terminal CAP residue I have to mention that I've already done this successfully with a gromacs version 4.0.5, but now I can't do it in gromacs 4.5.4... I have also added the 4 new residues into the file: residuetype.dat When I run the following line: g_pdb2gmx -f pol35.pdb -p top -o pol35 -ff my_gromos53a6 -ter It gives me: Using the My_gromos53a6 force field in directory ./my_gromos53a6.ff Opening force field file ./my_gromos53a6.ff/watermodels.dat Select the Water Model: 1: SPC simple point charge, recommended 2: SPC/E extended simple point charge 3: None 1 Opening force field file ./my_gromos53a6.ff/aminoacids.r2b Reading pol35.pdb... Read 'Glycine aRginine prOline Methionine Alanine Cystine Serine', 729 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 35 residues with 729 atoms chain #res #atoms 1 ' ' 35 729 All occupancies are one Opening force field file ./my_gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (my_gromos53a6) Opening force field file ./my_gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 119 Sorting it all out... Opening force field file ./my_gromos53a6.ff/aminoacids.hdb Opening force field file ./my_gromos53a6.ff/aminoacids.n.tdb Opening force field file ./my_gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up top.top to ./#top.top.1# Processing chain 1 (729 atoms, 35 residues) There are 28 donors and 0 acceptors There are 0 hydrogen bonds Identified residue TQL1 as a starting terminus. Warning: Residue VBR35 in chain has different type (Other) from starting residue TQL1 (Protein). Identified residue TEQ34 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for TQL-1 0: NH3+ 1: NH2 2: None 2 Start terminus TQL-1: None Select end terminus type for TEQ-34 0: COO- 1: COOH 2: None 2 End terminus TEQ-34: None --- Program g_pdb2gmx, VERSION 4.5.4 Source code file: /builddir/build/BUILD/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1035 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I don't understand why pdb2gmx takes the 34th residue as the last monomer when in fact it has 35... After the error I understood why pdb2gmx complains about: ..a dangling bond... But I do not know how to solve the problem I need that pdb2gmx uses my last 35th monomer as the last one... Any help will be appreciated... Sergio -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -- 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 building a polymer using pdb2gmx ....
Alberto Sergio Garay wrote: Hi All I'm building a polymer (heterodimer) using pdb2gmx tool. I have included in ffG53a6 the 4 building block I need (aminoacids.rtp in my own dir: ../my_ffG53a6..): X ... A-B-A-B-A-B-A-B-A-B-A ... Y X: starting CAP residue A: a monomer B: the other monomer Y: terminal CAP residue I have to mention that I've already done this successfully with a gromacs version 4.0.5, but now I can't do it in gromacs 4.5.4... I have also added the 4 new residues into the file: residuetype.dat When I run the following line: g_pdb2gmx -f pol35.pdb -p top -o pol35 -ff my_gromos53a6 -ter It gives me: Using the My_gromos53a6 force field in directory ./my_gromos53a6.ff Opening force field file ./my_gromos53a6.ff/watermodels.dat Select the Water Model: 1: SPC simple point charge, recommended 2: SPC/E extended simple point charge 3: None 1 Opening force field file ./my_gromos53a6.ff/aminoacids.r2b Reading pol35.pdb... Read 'Glycine aRginine prOline Methionine Alanine Cystine Serine', 729 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 35 residues with 729 atoms chain #res #atoms 1 ' ' 35 729 All occupancies are one Opening force field file ./my_gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (my_gromos53a6) Opening force field file ./my_gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 119 Sorting it all out... Opening force field file ./my_gromos53a6.ff/aminoacids.hdb Opening force field file ./my_gromos53a6.ff/aminoacids.n.tdb Opening force field file ./my_gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up top.top to ./#top.top.1# Processing chain 1 (729 atoms, 35 residues) There are 28 donors and 0 acceptors There are 0 hydrogen bonds Identified residue TQL1 as a starting terminus. Warning: Residue VBR35 in chain has different type (Other) from starting residue TQL1 (Protein). Identified residue TEQ34 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for TQL-1 0: NH3+ 1: NH2 2: None 2 Start terminus TQL-1: None Select end terminus type for TEQ-34 0: COO- 1: COOH 2: None 2 End terminus TEQ-34: None --- Program g_pdb2gmx, VERSION 4.5.4 Source code file: /builddir/build/BUILD/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1035 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I don't understand why pdb2gmx takes the 34th residue as the last monomer when in fact it has 35... After the error I understood why pdb2gmx complains about: ..a dangling bond... But I do not know how to solve the problem I need that pdb2gmx uses my last 35th monomer as the last one... The reason was printed to the screen: Warning: Residue VBR35 in chain has different type (Other) from starting residue TQL1 (Protein). Chains have to be all one type in order to be continuous. So, either all of your buildings blocks have to be defined as Protein or all of them have to be defined as Other. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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: Non-zero total charge
Hi, My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zero total charge: System has non-zero total charge: 5.70e+01 63 non-compensated ions in the single system... I wonder what this system is -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rendering such simulations less stable. As for SD, probably that causes sufficient damping of jitter introduced due to pressure coupling for it not to propagate and cause problems. But those are just my two cents (about 2.8 dollar cents with current rates :p). Cheers, Tsjerk On Thu, Sep 1, 2011 at 2:41 PM, chris.ne...@utoronto.ca wrote: I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] half double pair list method in GROMACS
Dear All, I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly --- gen-pairs = no ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 --- for AMBER99SB only 1 2no 1.0 0.16 --- for both GLYCAM et AMBER99SB ;1 2yes 1.0 1.0 -- for GLYCAM only #include ffnonbonded_mod.itp #include ffbonded.itp 2- For the surfactant, I have calculated the pair-types interactions manually with the comb-rule = 2 and divided the values /6 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files 3- For the peptide, I have calculated the pair-types interactions manually comb-rule = 2 and divided the values /10 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files. 4- In the surfactant topology file I have repeated 6 times the [pairs] directives 0.16*6 ~=10 5 - In the peptide topology file I have repeated 5 times the [pairs] directives 0.16*5 ~= 0.8333 Is it correct ? However I have a little doubt about gen-pairs directive should I have set it to no or yes. in a previous message with a similar problem, the gen directive was set yes http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Thank you for your help Stephane -- 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] GROMACS 4.5.4 keep crashing all the time
That all makes sense Tsjerk. I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1. Also, I'm still a little curious about a question that Itamar asked a few posts ago: If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Mark provided a good explanation about how this could be possible, but I've never seen lincs warnings or systems blowing up after 5 ns of equilibration. I fully realize that it may take even us of simulation to properly equilibrate statistical properties, but in my experience it is far outside of ordinary to require 5 ns of equilibration to avoid systems blowing up. Chris. -- original message -- Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rendering such simulations less stable. As for SD, probably that causes sufficient damping of jitter introduced due to pressure coupling for it not to propagate and cause problems. But those are just my two cents (about 2.8 dollar cents with current rates :p). Cheers, Tsjerk On Thu, Sep 1, 2011 at 2:41 PM, chris.neale at utoronto.ca wrote: I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk -- gmx-users mailing listgmx-users at 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 thewww interface or send it to gmx-users-request aGROMACS 4.5.4 keep crashing all the time Tsjerk Wassenaar tsjerkw at gmail.com Thu Sep 1 15:48:40 CEST 2011 * Previous message: [gmx-users] GROMACS 4.5.4 keep crashing all the time * Next message: [gmx-users] Non-zero total charge * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rendering such simulations less stable. As for SD, probably that causes sufficient damping of jitter introduced due to pressure coupling for it not to propagate and cause problems. But
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
On 2/09/2011 12:59 AM, chris.ne...@utoronto.ca wrote: That all makes sense Tsjerk. I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1. That tip might be a good thing for the wiki page on that. Also, I'm still a little curious about a question that Itamar asked a few posts ago: If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Mark provided a good explanation about how this could be possible, but I've never seen lincs warnings or systems blowing up after 5 ns of equilibration. I fully realize that it may take even us of simulation to properly equilibrate statistical properties, but in my experience it is far outside of ordinary to require 5 ns of equilibration to avoid systems blowing up. It's hard to say without more detail of how the extension occurred, and knowing how much ensemble data got lost. It's still conceivable some horrible mismatch occurred (e.g. virial over-written by some other data), but not really worth exploring properly. I'd just expect to have to re-equilibrate upon changing code version, and just not attempt such an extension. Mark Chris. -- original message -- Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rendering such simulations less stable. As for SD, probably that causes sufficient damping of jitter introduced due to pressure coupling for it not to propagate and cause problems. But those are just my two cents (about 2.8 dollar cents with current rates :p). Cheers, Tsjerk On Thu, Sep 1, 2011 at 2:41 PM, chris.neale at utoronto.ca wrote: I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk -- gmx-users mailing listgmx-users at 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 thewww interface or send it to gmx-users-request aGROMACS 4.5.4 keep crashing all the time Tsjerk Wassenaar tsjerkw at gmail.com Thu Sep 1 15:48:40 CEST 2011 * Previous message: [gmx-users] GROMACS 4.5.4 keep crashing all the time * Next message: [gmx-users] Non-zero total charge * Messages sorted by: [ date ] [ thread ] [
[gmx-users] half double pair list method in GROMACS
Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the manual and reading about pairs, gen-pairs, and pairtypes. I think that this is one case where you would benefit more from fully understanding how these parts work than from a direct answer to your question. If you are having problems, please provide a whole bunch more information on the problems that you are seeing. If, on the other hand, you are just looking for somebody other than me to comment on the accuracy of the April post, then that is perfectly fine with me, but you should state that. Chris. -- original message -- Dear All, I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly --- gen-pairs = no ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 --- for AMBER99SB only 1 2no 1.0 0.16 --- for both GLYCAM et AMBER99SB ;1 2yes 1.0 1.0 -- for GLYCAM only #include ffnonbonded_mod.itp #include ffbonded.itp 2- For the surfactant, I have calculated the pair-types interactions manually with the comb-rule = 2 and divided the values /6 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files 3- For the peptide, I have calculated the pair-types interactions manually comb-rule = 2 and divided the values /10 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files. 4- In the surfactant topology file I have repeated 6 times the [pairs] directives 0.16*6 ~=10 5 - In the peptide topology file I have repeated 5 times the [pairs] directives 0.16*5 ~= 0.8333 Is it correct ? However I have a little doubt about gen-pairs directive should I have set it to no or yes. in a previous message with a similar problem, the gen directive was set yes http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Thank you for your help Stephane -- 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] Non zero total charge
Hi, The genion command i used is genion -s genion.tpr -o ago_water_ions.gro -nn 6 I used this to add 6 CL ions and i got the following error: System has non-zero total charge: 5.70e+01 So i should add another 5 CL ions to neutralize the system? Many thanks, Munishika -- 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] Non zero total charge
Not 5. 57. Look at the exponent. On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia munishikaka...@yahoo.com wrote: Hi, The genion command i used is genion -s genion.tpr -o ago_water_ions.gro -nn 6 I used this to add 6 CL ions and i got the following error: System has non-zero total charge: 5.70e+01 So i should add another 5 CL ions to neutralize the system? Many thanks, Munishika -- 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
RE: [gmx-users] order parameter
Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the averaging correctly. 1. I take the carbons in each tail ( I neglect the 1st and the last as GROMACS does) , then I find the Hydrogens associated with it. 2. Then I do the PBC , normalise them and then take the angle, then calculate the order parameter. 3. finally I average them over the frames. I have gone through the procedure and still I am not getting the same profile as GROMACS gives. Is there anything else that I need to include in my calculations? Ramya From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: Wednesday, August 31, 2011 8:00 PM To: gmx-users@gromacs.org Subject: [gmx-users] order parameter Dear Ramya: Are you simulating all-atom lipids (with explicit hydrogen atoms on the acyl chain)? If not, then you missed a step in your description of what you have done (g_order, for example, ignores explicit hydrogen atoms so that it can act on united atom lipids). Not sure why PBC would be your step #3, after your step #2 was to find the angle. I suggest that you simply run trjconv -pbc mol on your trajectory file before you process it and then you no longer need to worry about PBC in your custom analysis tool. Once you have the angle, you must average it correctly. The equation is available in most papers that describe order parameters and is listed as a comment at the top of the gmx_order.c source file (in version 4.0.7 at least). If you want to get more help on your procedure after you have worked on this for a while, I suggest laying out your procedure very specifically. Your previous post, for example, was pretty loose with terminology when you described your method and there is quite a bit that one must assume. Chris. -- original message -- Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the ?CH molecular axis. 3. Took care of the periodic boundary conditions since I use NPT ensemble. But the code in gmx_order.c in GROMACS tries to do a lot of things other than this, as I don?t know C or C++ language that it is using, I don?t know what else I am supposed to include. Can someone please help me? Ramya -- 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] Non zero total charge
I believe your problem is that you do not understand scientific notation. 5.70e+01 = 57. Cl- has a charge of -1. Need I say more. On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia munishikaka...@yahoo.comwrote: Hi, The genion command i used is genion -s genion.tpr -o ago_water_ions.gro -nn 6 I used this to add 6 CL ions and i got the following error: System has non-zero total charge: 5.70e+01 So i should add another 5 CL ions to neutralize the system? Many thanks, Munishika -- 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] Half double pair list method in GROMACS
Hi Chris, Sorry to repost the same question, but I have really tested your method the last few weeks. My question about the gen-pairs directive come from the fact that I have read a message from you http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Where you detailed how to use the Berger and OPLS force fields together in the same system. By reading carefully the meaning of the gen-pairs directive, I found several errors in my force field. BYW in your previous message http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html In the step 3, I think there is a typo, it is values/10 instead of values/12. Am I right? Thank you again Stephane Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the manual and reading about pairs, gen-pairs, and pairtypes. I think that this is one case where you would benefit more from fully understanding how these parts work than from a direct answer to your question. If you are having problems, please provide a whole bunch more information on the problems that you are seeing. If, on the other hand, you are just looking for somebody other than me to comment on the accuracy of the April post, then that is perfectly fine with me, but you should state that. Chris. -- original message -- Dear All, I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly --- gen-pairs = no ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 --- for AMBER99SB only 1 2no 1.0 0.16 --- for both GLYCAM et AMBER99SB ;1 2yes 1.0 1.0 -- for GLYCAM only #include ffnonbonded_mod.itp #include ffbonded.itp 2- For the surfactant, I have calculated the pair-types interactions manually with the comb-rule = 2 and divided the values /6 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files 3- For the peptide, I have calculated the pair-types interactions manually comb-rule = 2 and divided the values /10 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files. 4- In the surfactant topology file I have repeated 6 times the [pairs] directives 0.16*6 ~=10 5 - In the peptide topology file I have repeated 5 times the [pairs] directives 0.16*5 ~= 0.8333 Is it correct ? However I have a little doubt about gen-pairs directive should I have set it to no or yes. in a previous message with a similar problem, the gen directive was set yes http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Thank you for your help Stephane -- 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] order parameter
Parthasarathi, Ramya wrote: Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the averaging correctly. 1. I take the carbons in each tail ( I neglect the 1st and the last as GROMACS does) , then I find the Hydrogens associated with it. 2. Then I do the PBC , normalise them and then take the angle, then calculate the order parameter. 3. finally I average them over the frames. I have gone through the procedure and still I am not getting the same profile as GROMACS gives. Is there anything else that I need to include in my calculations? There are several additional points to consider. 1. What type of differences are you getting? An image would be nice to see, otherwise no one has any chance of knowing what's going on. See point number 4 here: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette 2. Which results are more accurate with respect to experimental results, yours or those produced by g_order? 3. Are you analyzing saturated or unsaturated chains? There is a known problem with g_order's ability to calculated order parameters for unsaturated carbons, although I'm not sure if it's been filed on redmine yet. It's been discussed a number of times. -Justin Ramya From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: Wednesday, August 31, 2011 8:00 PM To: gmx-users@gromacs.org Subject: [gmx-users] order parameter Dear Ramya: Are you simulating all-atom lipids (with explicit hydrogen atoms on the acyl chain)? If not, then you missed a step in your description of what you have done (g_order, for example, ignores explicit hydrogen atoms so that it can act on united atom lipids). Not sure why PBC would be your step #3, after your step #2 was to find the angle. I suggest that you simply run trjconv -pbc mol on your trajectory file before you process it and then you no longer need to worry about PBC in your custom analysis tool. Once you have the angle, you must average it correctly. The equation is available in most papers that describe order parameters and is listed as a comment at the top of the gmx_order.c source file (in version 4.0.7 at least). If you want to get more help on your procedure after you have worked on this for a while, I suggest laying out your procedure very specifically. Your previous post, for example, was pretty loose with terminology when you described your method and there is quite a bit that one must assume. Chris. -- original message -- Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the ?CH molecular axis. 3. Took care of the periodic boundary conditions since I use NPT ensemble. But the code in gmx_order.c in GROMACS tries to do a lot of things other than this, as I don?t know C or C++ language that it is using, I don?t know what else I am supposed to include. Can someone please help me? Ramya -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] order parameter
In addition to Justin's comment about g_order being incorrect for unsaturated carbons, you won't ever get numerical agreement with g_order, even for saturated carbons, because g_order does not use your explicit hydrogens. g_order uses the positions of the carbons to rebuild the hydrogen positions assuming perfect tetrahedral geometry, which you certainly don't have in all cases when you use real hydrogens. There is a VMD tcl script that you can download that will compute order parameters from real hydrogen atoms. perhaps you should try to compare to that. Chris. -- original message -- Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the averaging correctly. 1. I take the carbons in each tail ( I neglect the 1st and the last as GROMACS does) , then I find the Hydrogens associated with it. 2. Then I do the PBC , normalise them and then take the angle, then calculate the order parameter. 3. finally I average them over the frames. I have gone through the procedure and still I am not getting the same profile as GROMACS gives. Is there anything else that I need to include in my calculations? Ramya From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at utoronto.ca] Sent: Wednesday, August 31, 2011 8:00 PM To: gmx-users at gromacs.org Subject: [gmx-users] order parameter Dear Ramya: Are you simulating all-atom lipids (with explicit hydrogen atoms on the acyl chain)? If not, then you missed a step in your description of what you have done (g_order, for example, ignores explicit hydrogen atoms so that it can act on united atom lipids). Not sure why PBC would be your step #3, after your step #2 was to find the angle. I suggest that you simply run trjconv -pbc mol on your trajectory file before you process it and then you no longer need to worry about PBC in your custom analysis tool. Once you have the angle, you must average it correctly. The equation is available in most papers that describe order parameters and is listed as a comment at the top of the gmx_order.c source file (in version 4.0.7 at least). If you want to get more help on your procedure after you have worked on this for a while, I suggest laying out your procedure very specifically. Your previous post, for example, was pretty loose with terminology when you described your method and there is quite a bit that one must assume. Chris. -- original message -- Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the ?CH molecular axis. 3. Took care of the periodic boundary conditions since I use NPT ensemble. But the code in gmx_order.c in GROMACS tries to do a lot of things other than this, as I don?t know C or C++ language that it is using, I don?t know what else I am supposed to include. Can someone please help me? Ramya -- -- 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] Half double pair list method in GROMACS
It's a typo, but it's in the discussion and not in the do this part of the method so I decided not to mention it. I don't see another question in this post, so I hope that you have figured things out. Note that I have never tested the exact implementation that I suggested in that April email. It seems like it should work just fine, but it is numerically different than the OPLS/Berger combination so there is no way to be sure until you check the energies as I suggested. I'd be interested to have you report back on the energy matching once you have done the tests. Good luck, Chris. -- original message -- Hi Chris, Sorry to repost the same question, but I have really tested your method the last few weeks. My question about the gen-pairs directive come from the fact that I have read a message from you http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Where you detailed how to use the Berger and OPLS force fields together in the same system. By reading carefully the meaning of the gen-pairs directive, I found several errors in my force field. BYW in your previous message http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html In the step 3, I think there is a typo, it is values/10 instead of values/12. Am I right? Thank you again Stephane Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the manual and reading about pairs, gen-pairs, and pairtypes. I think that this is one case where you would benefit more from fully understanding how these parts work than from a direct answer to your question. If you are having problems, please provide a whole bunch more information on the problems that you are seeing. If, on the other hand, you are just looking for somebody other than me to comment on the accuracy of the April post, then that is perfectly fine with me, but you should state that. Chris. -- original message -- Dear All, I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly --- gen-pairs = no ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 --- for AMBER99SB only 1 2no 1.0 0.16 --- for both GLYCAM et AMBER99SB ;1 2yes 1.0 1.0 -- for GLYCAM only #include ffnonbonded_mod.itp #include ffbonded.itp 2- For the surfactant, I have calculated the pair-types interactions manually with the comb-rule = 2 and divided the values /6 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files 3- For the peptide, I have calculated the pair-types interactions manually comb-rule = 2 and divided the values /10 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files. 4- In the surfactant topology file I have repeated 6 times the [pairs] directives 0.16*6 ~=10 5 - In the peptide topology file I have repeated 5 times the [pairs] directives 0.16*5 ~= 0.8333 Is it correct ? However I have a little doubt about gen-pairs directive should I have set it to no or yes. in a previous message with a similar problem, the gen directive was set yes http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Thank you for your help Stephane -- 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] GROMACS 4.5.4 keep crashing all the time
That seems possible Mark. I had actually assumed that Itamar extracted a .gro from the 4.0.7 simulations and created a new .tpr with 4.5.4 grompp. If that was the case, then I would still be surprised that it had instability problems. One sees a lot of charmm papers where people do slow heating, but my experience with gromacs is that not too many people worry about maintaining the velocities from their NVT simulations for their NPT simulations (or restrained - unrestrained) and that it works out just fine. On the other hand, I don't see too many gromacs reaction field studies either, so perhaps it all makes sense to those who use these methods. Thanks again, Chris. On 2/09/2011 12:59 AM, chris.neale at utoronto.ca wrote: That all makes sense Tsjerk. I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1. That tip might be a good thing for the wiki page on that. Also, I'm still a little curious about a question that Itamar asked a few posts ago: If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Mark provided a good explanation about how this could be possible, but I've never seen lincs warnings or systems blowing up after 5 ns of equilibration. I fully realize that it may take even us of simulation to properly equilibrate statistical properties, but in my experience it is far outside of ordinary to require 5 ns of equilibration to avoid systems blowing up. It's hard to say without more detail of how the extension occurred, and knowing how much ensemble data got lost. It's still conceivable some horrible mismatch occurred (e.g. virial over-written by some other data), but not really worth exploring properly. I'd just expect to have to re-equilibrate upon changing code version, and just not attempt such an extension. Mark Chris. -- original message -- Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rendering such simulations less stable. As for SD, probably that causes sufficient damping of jitter introduced due to pressure coupling for it not to propagate and cause problems. But those are just my two cents (about 2.8 dollar cents with current rates :p). Cheers, Tsjerk On Thu, Sep 1, 2011 at 2:41 PM, chris.neale at utoronto.ca wrote: I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it
RE: [gmx-users] order parameter
[X] Hi Justin, Thanks for the reply, and this is the graph, the red curve is what GROMACS gives, the blue curve is what I get.. yes I am considering the unsaturated carbons in to account. I have to see which is closer to the experimental result. Hi Chris, Thanks for the information , I will surely try the VMD tcl script and compute the order parameters and compare. If there is anything else that you suggest kindly let me know , it will be very helpful for me. Thanks again Ramya There are several additional points to consider. 1. What type of differences are you getting? An image would be nice to see, otherwise no one has any chance of knowing what's going on. See point number 4 here: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette 2. Which results are more accurate with respect to experimental results, yours or those produced by g_order? 3. Are you analyzing saturated or unsaturated chains? There is a known problem with g_order's ability to calculated order parameters for unsaturated carbons, although I'm not sure if it's been filed on redmine yet. It's been discussed a number of times. -Justin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: Thursday, September 01, 2011 1:35 PM To: gmx-users@gromacs.org Subject: [gmx-users] order parameter In addition to Justin's comment about g_order being incorrect for unsaturated carbons, you won't ever get numerical agreement with g_order, even for saturated carbons, because g_order does not use your explicit hydrogens. g_order uses the positions of the carbons to rebuild the hydrogen positions assuming perfect tetrahedral geometry, which you certainly don't have in all cases when you use real hydrogens. There is a VMD tcl script that you can download that will compute order parameters from real hydrogen atoms. perhaps you should try to compare to that. Chris. -- original message -- Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the averaging correctly. 1. I take the carbons in each tail ( I neglect the 1st and the last as GROMACS does) , then I find the Hydrogens associated with it. 2. Then I do the PBC , normalise them and then take the angle, then calculate the order parameter. 3. finally I average them over the frames. I have gone through the procedure and still I am not getting the same profile as GROMACS gives. Is there anything else that I need to include in my calculations? Ramya From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at utoronto.ca] Sent: Wednesday, August 31, 2011 8:00 PM To: gmx-users at gromacs.org Subject: [gmx-users] order parameter Dear Ramya: Are you simulating all-atom lipids (with explicit hydrogen atoms on the acyl chain)? If not, then you missed a step in your description of what you have done (g_order, for example, ignores explicit hydrogen atoms so that it can act on united atom lipids). Not sure why PBC would be your step #3, after your step #2 was to find the angle. I suggest that you simply run trjconv -pbc mol on your trajectory file before you process it and then you no longer need to worry about PBC in your custom analysis tool. Once you have the angle, you must average it correctly. The equation is available in most papers that describe order parameters and is listed as a comment at the top of the gmx_order.c source file (in version 4.0.7 at least). If you want to get more help on your procedure after you have worked on this for a while, I suggest laying out your procedure very specifically. Your previous post, for example, was pretty loose with terminology when you described your method and there is quite a bit that one must assume. Chris. -- original message -- Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the ?CH molecular axis. 3. Took care of the periodic boundary conditions since I use NPT ensemble. But the code in gmx_order.c in GROMACS tries to do a lot of things other than this, as I don?t know C or C++ language that it is using, I don?t know what else I am supposed to include. Can someone please help me? Ramya -- -- 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
Re: [gmx-users] order parameter
Parthasarathi, Ramya wrote: Hi Justin, Thanks for the reply, and this is the graph, the red curve is what GROMACS gives, the blue curve is what I get.. yes I am considering the unsaturated carbons in to account. I have to see which is closer to the experimental result. I can't see any image. Please heed the instructions I provided earlier for proper sharing of images. Embedding usually doesn't work for many mail clients, especially those of us who get plain text. -Justin Hi Chris, Thanks for the information , I will surely try the VMD tcl script and compute the order parameters and compare. If there is anything else that you suggest kindly let me know , it will be very helpful for me. Thanks again Ramya There are several additional points to consider. 1. What type of differences are you getting? An image would be nice to see, otherwise no one has any chance of knowing what's going on. See point number 4 here: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette 2. Which results are more accurate with respect to experimental results, yours or those produced by g_order? 3. Are you analyzing saturated or unsaturated chains? There is a known problem with g_order's ability to calculated order parameters for unsaturated carbons, although I'm not sure if it's been filed on redmine yet. It's been discussed a number of times. -Justin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: Thursday, September 01, 2011 1:35 PM To: gmx-users@gromacs.org Subject: [gmx-users] order parameter In addition to Justin's comment about g_order being incorrect for unsaturated carbons, you won't ever get numerical agreement with g_order, even for saturated carbons, because g_order does not use your explicit hydrogens. g_order uses the positions of the carbons to rebuild the hydrogen positions assuming perfect tetrahedral geometry, which you certainly don't have in all cases when you use real hydrogens. There is a VMD tcl script that you can download that will compute order parameters from real hydrogen atoms. perhaps you should try to compare to that. Chris. -- original message -- Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the averaging correctly. 1. I take the carbons in each tail ( I neglect the 1st and the last as GROMACS does) , then I find the Hydrogens associated with it. 2. Then I do the PBC , normalise them and then take the angle, then calculate the order parameter. 3. finally I average them over the frames. I have gone through the procedure and still I am not getting the same profile as GROMACS gives. Is there anything else that I need to include in my calculations? Ramya From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at utoronto.ca] Sent: Wednesday, August 31, 2011 8:00 PM To: gmx-users at gromacs.org Subject: [gmx-users] order parameter Dear Ramya: Are you simulating all-atom lipids (with explicit hydrogen atoms on the acyl chain)? If not, then you missed a step in your description of what you have done (g_order, for example, ignores explicit hydrogen atoms so that it can act on united atom lipids). Not sure why PBC would be your step #3, after your step #2 was to find the angle. I suggest that you simply run trjconv -pbc mol on your trajectory file before you process it and then you no longer need to worry about PBC in your custom analysis tool. Once you have the angle, you must average it correctly. The equation is available in most papers that describe order parameters and is listed as a comment at the top of the gmx_order.c source file (in version 4.0.7 at least). If you want to get more help on your procedure after you have worked on this for a while, I suggest laying out your procedure very specifically. Your previous post, for example, was pretty loose with terminology when you described your method and there is quite a bit that one must assume. Chris. -- original message -- Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the ?CH molecular axis. 3. Took care of the periodic boundary conditions since I use NPT ensemble. But the code in gmx_order.c in GROMACS tries to do a lot of things other than this, as I don?t know C or C++ language that it is using, I don?t know what else I am supposed to include. Can someone please help me?
[gmx-users] pdb2gmx response time
Hi All, when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /share/apps/gromacs407/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /share/apps/gromacs407/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /share/apps/gromacs407/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /share/apps/gromacs407/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /share/apps/gromacs407/share/gromacs/top/elements.dat Entries in elements.dat: 218 Opening library file /share/apps/gromacs407/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 14 atoms chain #res #atoms 1 '-' 1 14 No occupancies in AA.gro Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.atp Atomtype 1 Has anyone come across this before? 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] Half double pair list method in GROMACS
Chris, Thank you for your confirmation. I did the changes. I am currently doing some tests, I will send you a feedback about the results off-list (if you want) shortly. A bientôt Stéphane Message: 1 Date: Thu, 01 Sep 2011 14:38:53 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Half double pair list method in GROMACS To: gmx-users@gromacs.org Message-ID: 20110901143853.537ln0dj94w4w...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed It's a typo, but it's in the discussion and not in the do this part of the method so I decided not to mention it. I don't see another question in this post, so I hope that you have figured things out. Note that I have never tested the exact implementation that I suggested in that April email. It seems like it should work just fine, but it is numerically different than the OPLS/Berger combination so there is no way to be sure until you check the energies as I suggested. I'd be interested to have you report back on the energy matching once you have done the tests. Good luck, Chris. -- original message -- Hi Chris, Sorry to repost the same question, but I have really tested your method the last few weeks. My question about the gen-pairs directive come from the fact that I have read a message from you http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Where you detailed how to use the Berger and OPLS force fields together in the same system. By reading carefully the meaning of the gen-pairs directive, I found several errors in my force field. BYW in your previous message http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html In the step 3, I think there is a typo, it is values/10 instead of values/12. Am I right? Thank you again Stephane Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the manual and reading about pairs, gen-pairs, and pairtypes. I think that this is one case where you would benefit more from fully understanding how these parts work than from a direct answer to your question. If you are having problems, please provide a whole bunch more information on the problems that you are seeing. If, on the other hand, you are just looking for somebody other than me to comment on the accuracy of the April post, then that is perfectly fine with me, but you should state that. Chris. -- original message -- Dear All, I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly --- gen-pairs = no ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 --- for AMBER99SB only 1 2no 1.0 0.16 --- for both GLYCAM et AMBER99SB ;1 2yes 1.0 1.0 -- for GLYCAM only #include ffnonbonded_mod.itp #include ffbonded.itp 2- For the surfactant, I have calculated the pair-types interactions manually with the comb-rule = 2 and divided the values /6 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files 3- For the peptide, I have calculated the pair-types interactions manually comb-rule = 2 and divided the values /10 and added these values in [pairtypes] section in the ffnonbonded_mod.itp files. 4- In the surfactant topology file I have repeated 6 times the [pairs] directives 0.16*6 ~=10 5 - In the peptide topology file I have repeated 5 times the [pairs] directives 0.16*5 ~= 0.8333 Is it correct ? However I have a little doubt about gen-pairs directive should I have set it to no or yes. in a previous message with a similar problem, the gen directive was set yes http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Thank you for your help Stephane -- 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] pdb2gmx response time
Yao Yao wrote: Hi All, when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /share/apps/gromacs407/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /share/apps/gromacs407/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /share/apps/gromacs407/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /share/apps/gromacs407/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /share/apps/gromacs407/share/gromacs/top/elements.dat Entries in elements.dat: 218 Opening library file /share/apps/gromacs407/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 14 atoms chain #res #atoms 1 '-' 1 14 No occupancies in AA.gro Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.atp Atomtype 1 Has anyone come across this before? There are a variety of reasons this could be happening. You haven't provided your command line or information about terminus selection, which could be pertinent in the case of a single residue. Have you modified the .atp file in any way? There was an old bug that might have affected this, but I can't remember if it was specific to the 4.5.x series or not. Otherwise, upgrade to version 4.5.4 and try again. Troubleshooting two-year-old software is not terribly productive, especially when newer versions may have resolved the issue. -Justin Thanks, Yao -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] order parameter
Parthasarathi, Ramya wrote: I am sorry I pasted the picture do not know whether it got posted or not so I am attching the figure in JPEG format. Your code is producing completely unreasonable values, so I would suspect some error in whatever you've done. In this case, Gromacs is providing a very reasonable outcome. -Justin Ramya From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, September 01, 2011 2:31 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] order parameter Parthasarathi, Ramya wrote: Hi Justin, Thanks for the reply, and this is the graph, the red curve is what GROMACS gives, the blue curve is what I get.. yes I am considering the unsaturated carbons in to account. I have to see which is closer to the experimental result. I can't see any image. Please heed the instructions I provided earlier for proper sharing of images. Embedding usually doesn't work for many mail clients, especially those of us who get plain text. -Justin Hi Chris, Thanks for the information , I will surely try the VMD tcl script and compute the order parameters and compare. If there is anything else that you suggest kindly let me know , it will be very helpful for me. Thanks again Ramya There are several additional points to consider. 1. What type of differences are you getting? An image would be nice to see, otherwise no one has any chance of knowing what's going on. See point number 4 here: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette 2. Which results are more accurate with respect to experimental results, yours or those produced by g_order? 3. Are you analyzing saturated or unsaturated chains? There is a known problem with g_order's ability to calculated order parameters for unsaturated carbons, although I'm not sure if it's been filed on redmine yet. It's been discussed a number of times. -Justin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: Thursday, September 01, 2011 1:35 PM To: gmx-users@gromacs.org Subject: [gmx-users] order parameter In addition to Justin's comment about g_order being incorrect for unsaturated carbons, you won't ever get numerical agreement with g_order, even for saturated carbons, because g_order does not use your explicit hydrogens. g_order uses the positions of the carbons to rebuild the hydrogen positions assuming perfect tetrahedral geometry, which you certainly don't have in all cases when you use real hydrogens. There is a VMD tcl script that you can download that will compute order parameters from real hydrogen atoms. perhaps you should try to compare to that. Chris. -- original message -- Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the averaging correctly. 1. I take the carbons in each tail ( I neglect the 1st and the last as GROMACS does) , then I find the Hydrogens associated with it. 2. Then I do the PBC , normalise them and then take the angle, then calculate the order parameter. 3. finally I average them over the frames. I have gone through the procedure and still I am not getting the same profile as GROMACS gives. Is there anything else that I need to include in my calculations? Ramya From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at utoronto.ca] Sent: Wednesday, August 31, 2011 8:00 PM To: gmx-users at gromacs.org Subject: [gmx-users] order parameter Dear Ramya: Are you simulating all-atom lipids (with explicit hydrogen atoms on the acyl chain)? If not, then you missed a step in your description of what you have done (g_order, for example, ignores explicit hydrogen atoms so that it can act on united atom lipids). Not sure why PBC would be your step #3, after your step #2 was to find the angle. I suggest that you simply run trjconv -pbc mol on your trajectory file before you process it and then you no longer need to worry about PBC in your custom analysis tool. Once you have the angle, you must average it correctly. The equation is available in most papers that describe order parameters and is listed as a comment at the top of the gmx_order.c source file (in version 4.0.7 at least). If you want to get more help on your procedure after you have worked on this for a while, I suggest laying out your procedure very specifically. Your previous post, for example, was pretty loose with terminology when you described your method and there is quite a bit that one must assume. Chris. -- original message -- Hi, I am
[gmx-users] anisotripic polarization in water model
Dear GMX users, I am using GMX 4.5.3 I wnat to implement the anisotropic polarization of water, i.e. the polarizability is different in each direction. Is is possible with GROMACS? Can anybody help me how to do it? Thank you in advanced for all your helps/comments. Best, Jae H. Park === Jae Hyun Park, Ph.D. Physics Division Oak Ridge National Laboratory P.O. Box 2008, MS-6372 Oak Ridge, TN 37831 Phone (865) 241-1482 E-mail pa...@ornl.gov-- 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] atom type not in rtp entry
Hi, I get the following error message when i try to pdb2gmx my protein file: Fatal error: Atom D21 in residue LEU 1 was not found in rtp entry LEU with 11 atoms while sorting atoms. I wonder which of these need to be changed! Thank you for your time. __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __ -- 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] atom type not in rtp entry
On 2/09/2011 11:47 AM, Sweta Iyer wrote: Hi, I get the following error message when i try to pdb2gmx my protein file: Fatal error: Atom D21 in residue LEU 1 was not found in rtp entry LEU with 11 atoms while sorting atoms. I wonder which of these need to be changed! Please describe your overall simulation objective and copy and paste your command line. Not giving them forces us to choose between guessing how to help you, or choosing not to do so. The atom names and residue names in your coordinate file have to be matched by pdb2gmx with the contents of the .rtp file. Apparently you have a weirdly named atom in a leucine residue. You should be fixing your atom and/or residue naming scheme, but without the above information, that's all that can 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
