[gmx-users] NVT equilibration
Dear gmx users, I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K. Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error: Fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally? Cheers, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] NVT equilibration
Are you running NVT with position restraint dynamics of your protein? Your system is probably not minimizied enough. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Thursday, August 09, 2012 1:23 PM To: Discussion list for GROMACS users Subject: [gmx-users] NVT equilibration Dear gmx users, I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K. Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error: Fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally? Cheers, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT equilibration
Parts of your system shifted too much (in Y dimension) for PME to handle. What happens to the system up to the point of the crash? How large is the system (particle count) vs. # of PME nodes used? Could be your system is too small for the # of PME nodes used Is the protein somehow interacting with its own PBC images? Is there enough water in the box to shield the protein from seeing itself in the next box over - it's probably safe to go with a thickness of water around the protein that is equal to the rcoulomb and rvdw cutoffs (that way you really get 2x the distance between protein images). On 2012-08-09 05:23:17AM -0700, Shima Arasteh wrote: Dear gmx users, I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K. Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error: Fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally? Cheers, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT equilibration
Thanks for replies. Some bonds are rotated more than 30 degrees ,as it's written just before turning off the equilibration. Is this over-rotation also included in interaction with PBC images? Am I supposed to change the rcoulomb and rvdw cutoffs? How would I be sure of a correct changes? Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, August 9, 2012 5:08 PM Subject: Re: [gmx-users] NVT equilibration Parts of your system shifted too much (in Y dimension) for PME to handle. What happens to the system up to the point of the crash? How large is the system (particle count) vs. # of PME nodes used? Could be your system is too small for the # of PME nodes used Is the protein somehow interacting with its own PBC images? Is there enough water in the box to shield the protein from seeing itself in the next box over - it's probably safe to go with a thickness of water around the protein that is equal to the rcoulomb and rvdw cutoffs (that way you really get 2x the distance between protein images). On 2012-08-09 05:23:17AM -0700, Shima Arasteh wrote: Dear gmx users, I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K. Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error: Fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally? Cheers, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT equilibration
On 2012-08-09 05:56:46AM -0700, Shima Arasteh wrote: Thanks for replies. Some bonds are rotated more than 30 degrees ,as it's written just before turning off the equilibration. Is this over-rotation also included in interaction with PBC images? So the system crashed before LINCS did. Perhaps more energy minimization would be helpful? See what atoms/residues were misbehaving (when LINCS throws those errors, it gives you the atom #) and look at its neighbors to see what sort of large forces might arise. Am I supposed to change the rcoulomb and rvdw cutoffs? How would I be sure of a correct changes? You are supposed to use the cutoffs appropriate for your forcefield. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, August 9, 2012 5:08 PM Subject: Re: [gmx-users] NVT equilibration Parts of your system shifted too much (in Y dimension) for PME to handle. What happens to the system up to the point of the crash? How large is the system (particle count) vs. # of PME nodes used? Could be your system is too small for the # of PME nodes used Is the protein somehow interacting with its own PBC images? Is there enough water in the box to shield the protein from seeing itself in the next box over - it's probably safe to go with a thickness of water around the protein that is equal to the rcoulomb and rvdw cutoffs (that way you really get 2x the distance between protein images). On 2012-08-09 05:23:17AM -0700, Shima Arasteh wrote: Dear gmx users, I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K. Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error: Fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally? Cheers, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] nvt equilibration output
Respected sir, I am studying about micelle formation .. After setting box and adding water i went for energy minimization and then went for nvt equilibration for 1ns. when i visualized my nvt.pdb file, i found that my protein comes together and formed three micelle like structure. but my box got separated. i dono why i got two separate box. can anyone tell me why this occurs.. i tried many times.. but still i am getting the same.. but i already performed dynamics for 30 monomers.. that time it went well.. now i am getting my output like this.. i checked the system temperature.. its in equilibrium at 299.9k. please help me with your answer.. Thanking you. -- 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] nvt equilibration output
On 16/05/2012 4:18 PM, priya thiyagarajan wrote: Respected sir, I am studying about micelle formation .. After setting box and adding water i went for energy minimization and then went for nvt equilibration for 1ns. when i visualized my nvt.pdb file, i found that my protein comes together and formed three micelle like structure. but my box got separated. i dono why i got two separate box. can anyone tell me why this occurs.. i tried many times.. but still i am getting the same.. but i already performed dynamics for 30 monomers.. that time it went well.. now i am getting my output like this.. i checked the system temperature.. its in equilibrium at 299.9k. Whatever you're observing is almost certainly normal, and you need to be sure you understand http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. The advice there, and perhaps further options you can see in trjconv -h will be necessary to manipulate the trajectory so that it looks the way you want it to. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nvt equilibration output
Hi Priya, My query is different than your problem .. I wondered Is you use position restrained in nvt...?? In position restrained protein comes togather or you remove position restraind ... Sorry for trouble you... With Best wishes, Rama David -- 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] nvt equilibration output
Respected sir, thanks for your kind reply... i applied position restrain during nvt step sir.. Thanking you, -- 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] NVT Equilibration
Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs tcoupl = V-rescale ; modified Berendsen thermostat The system converged quickly to the reference value (after 2-3ps). Should it converge more slowly and gradually? In the case how could fix it? Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT Equilibration
Alex Jemulin wrote: Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs tcoupl = V-rescale ; modified Berendsen thermostat The system converged quickly to the reference value (after 2-3ps). Should it converge more slowly and gradually? In the case how could fix it? It should likely converge very quickly. I see nothing wrong. -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] NVT Equilibration
Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs tcoupl = V-rescale ; modified Berendsen thermostat The system converged quickly to the reference value (after 2-3ps). Should it converge more slowly and gradually? In the case how could fix it? Thanks-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] nvt equilibration
Hello Justin, I am curious to know that why have nvt equilibration is not performed in umbrella sampling? Thanx. -- 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] nvt equilibration
swati patel wrote: Hello Justin, I am curious to know that why have nvt equilibration is not performed in umbrella sampling? NVT is not necessarily required. I just happen to know that the system used in the tutorial is rather robust and can proceed straight to NPT. Typically NVT is advisable. -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] NVT Equilibration
*Dear All, But I scaled the solvent box according to the density using editconf_d command line. Then I carried out EM and NVT equilibration.* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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] NVT Equilibration
Ravi Kumar Venkatraman wrote: *Dear All, But I scaled the solvent box according to the density using editconf_d command line. Then I carried out EM and NVT equilibration.* Scaling the box with editconf simply scales the coordinates of the molecules in it, which may or may not produce a physically stable condition. Building a better starting box is the proper solution, as Dallas suggested. -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
RE: [gmx-users] NVT Equilibration
Ravi, not entirely sure what you are actually doing / aiming to do, but another option is to run the system NPT, which means the box size will scale to give the correct pressure / density, then you take that and run your NVT run. But that means you will end up with possibly a substantially smaller box, which may be an issue. But, closer you are to the correct starting point when you build the box the better. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, 6 October 2011 9:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] NVT Equilibration Ravi Kumar Venkatraman wrote: *Dear All, But I scaled the solvent box according to the density using editconf_d command line. Then I carried out EM and NVT equilibration.* Scaling the box with editconf simply scales the coordinates of the molecules in it, which may or may not produce a physically stable condition. Building a better starting box is the proper solution, as Dallas suggested. -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 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] NVT Equilibration
Concur. I just used this approach to equilibrate a box of water/acetonitrile. If your box shrinks too much, you can probably use editconf and genbox to replicate the equilibrated box into a larger box of arbitrary size and shape. MZ On Thu, Oct 6, 2011 at 4:36 PM, Dallas Warren dallas.war...@monash.edu wrote: Ravi, not entirely sure what you are actually doing / aiming to do, but another option is to run the system NPT, which means the box size will scale to give the correct pressure / density, then you take that and run your NVT run. But that means you will end up with possibly a substantially smaller box, which may be an issue. But, closer you are to the correct starting point when you build the box the better. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- 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] NVT equilibration of ethanol in OPLSAA ff
Dear All, I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of 512 molecules (as of Bevan's gromacs tutorial) and then I scaled the solvent box for the density of ethanol (785.22 g/l) at 298.15. Before creatin solvent box I EM the isolated solvent molecule, then I used that molecule to generate the solvent box. Then I EM the solvent box 512 molecules.Followin are the parameters for EM of Solvent box. ; RUN CONTROL PARAMETERS integrator = steep ; start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 1 nstlist = 10 rlist= 1.1 coulombtype = pme pme_order= 4 fourierspacing = 0.16 rcoulomb = 1.1 vdw-type = cut-off rvdw = 1.1 nstenergy= 10 ; ENERGY MINIMIZATION OPTIONS emtol= 1000.0 emstep = 0.1 I saw the em.xvg file it is minimized well. Then I started NVT equilibration with lincs constraints for hbonds at timesteps of 0.2 fs and runned for 5 ps. The resultant configuration shows that most of the molecules were together at region of box and there was some void inside the box. I used cut-off of 1.1 nm for electrostatic and VdW interactions. I didn't use any shift or switch function. (can anybody suggest me a good tutorial to understand the judicious use of this functions.) Please help me sort this problem. If you need further details I am ready to send you. Thank you. With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, INDIA. -- 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] NVT equilibration of ethanol in OPLSAA ff
On 5/10/2011 6:36 PM, Ravi Kumar Venkatraman wrote: Dear All, I downloaded ethanol.pdb file from prodrg server (all-atom). I used ethanol.itp file that was in oplsaa.ff directory of gromacs to create topology file for ethanol. I used genconf_d command to generate solvent box of 512 molecules (as of Bevan's gromacs tutorial) and then I scaled the solvent box for the density of ethanol (785.22 g/l) at 298.15. Did you view the system+box at this stage? What were your actual commands? You will get much more effective help if you provide an excess of information, than if you expect people to guess the right follow-up questions when they have little information. Before creatin solvent box I EM the isolated solvent molecule, then I used that molecule to generate the solvent box. Then I EM the solvent box 512 molecules.Followin are the parameters for EM of Solvent box. ; RUN CONTROL PARAMETERS integrator = steep ; start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 1 nstlist = 10 rlist= 1.1 coulombtype = pme pme_order= 4 fourierspacing = 0.16 rcoulomb = 1.1 vdw-type = cut-off rvdw = 1.1 nstenergy= 10 ; ENERGY MINIMIZATION OPTIONS emtol= 1000.0 emstep = 0.1 I saw the em.xvg file it is minimized well. Then I started NVT equilibration with lincs constraints for hbonds at timesteps of 0.2 fs and runned for 5 ps. The resultant configuration shows that most of the molecules were together at region of box and there was some void inside the box. I used cut-off of 1.1 nm for electrostatic and VdW interactions. I didn't use any shift or switch function. (can anybody suggest me a good tutorial to understand the judicious use of this functions.) What you've done is fine so far. There is no clear path for these choices. Ideally you should consider the scheme under which the force field was parameterized, and how it has been successfully used since, and do something very similar. Mark Please help me sort this problem. If you need further details I am ready to send you. Thank you. With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, INDIA. -- 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] NVT equilibration.
Dear All, My commands where, genconf_d -f ethanol.gro -o ethanol512.gro -nbox 8 8 8 editconf_d -f eth512.gro -density 785.22 -o den.gro I saw the den.gro by using VMD. I saw only as points but not the molecules. EM: grompp_d -f em.mdp -c den.gro -p ethanol.top -o em.tpr mdrun_d -deffnm em I saw em.gro using VMD. Now I see ethanol molecules arranged all over thebox in order. *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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] NVT equilibration of Ethanol in OPLSAA.
*Dear all, I have been trying to generate pre-equilibrated ethanol solvent box of 512 molecules in **OPLSAA ff. I used ethanol.itp in oplsaa.ff directory for generating the topology file for ethanol. After NVT equilibration some of the molecules get aggregated and there is some void in the box. I tried running at faster time scales like 0.2 fs then also I was getting the same. Please help me to overcome this problem. With regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA.* -- 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] NVT equilibration of Ethanol in OPLSAA.
On 4/10/2011 6:16 PM, Ravi Kumar Venkatraman wrote: *Dear all, I have been trying to generate pre-equilibrated ethanol solvent box of 512 molecules in **OPLSAA ff. I used ethanol.itp in oplsaa.ff directory for generating the topology file for ethanol. After NVT equilibration some of the molecules get aggregated and there is some void in the box. I tried running at faster time scales like 0.2 fs then also I was getting the same. Please help me to overcome this problem.* You should follow the suggestions here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation. Even if you have, we'd need a lot more detailed information about your procedure and parameters to be able to guess what might have gone wrong. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] NVT equilibration of Ethanol in OPLSAA.
Sounds very much like you have an insufficient number of molecules in the box to fill it up. If you look at the pressure data for the simulation, I suspect you will find that it is negative, the box wants to decrease in volume. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ravi Kumar Venkatraman Sent: Tuesday, 4 October 2011 6:17 PM To: gmx-users@gromacs.org Subject: [gmx-users] NVT equilibration of Ethanol in OPLSAA. Dear all, I have been trying to generate pre-equilibrated ethanol solvent box of 512 molecules in OPLSAA ff. I used ethanol.itp in oplsaa.ff directory for generating the topology file for ethanol. After NVT equilibration some of the molecules get aggregated and there is some void in the box. I tried running at faster time scales like 0.2 fs then also I was getting the same. Please help me to overcome this problem. With regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. -- 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] NVT Equilibration getting blown up
Dear All, I am doing NVT equilibration for Ethanol of cubic box of side length 6.10346 nm in OPLSAA ff after doing the Energy Minimisation. My system getting blown up when I do NVT equilibration. Following are the some parameters that I have mentioned in *.mdp files, 100 ps run in 2 fs steps. cut-off length was 1.0 nm. Berendsen Thermostat at 298.15 k with 0.1 ps time constant. lincs constraint for all-bonds. Please suggest me something so that I can simulate without blowing up my system. Thank you, With Regards, Ravi Kumar Venkatraman. -- 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] NVT Equilibration getting blown up
On 1/10/2011 5:09 PM, Ravi Kumar Venkatraman wrote: Dear All, I am doing NVT equilibration for Ethanol of cubic box of side length 6.10346 nm in OPLSAA ff after doing the Energy Minimisation. My system getting blown up when I do NVT equilibration. Following are the some parameters that I have mentioned in *.mdp files, 100 ps run in 2 fs steps. cut-off length was 1.0 nm. Berendsen Thermostat at 298.15 k with 0.1 ps time constant. lincs constraint for all-bonds. Those are all normal enough, but smaller timesteps can help during equilibration. Other standard advice here http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System 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
[gmx-users] NVT equilibration of DMSO solvent (Charmm all-atom force field)
Dear GROMACS users, I have generated a 4*4*4 octahedral DMSO box containing 64 molecules (Charmm all-atom force field) which need to be NVT equilibrated in order to pass it for usage in genbox. Could one of you provide info on how to do the NVT and periodic boundary equilibration to remove the residual ordering of the solvent? Thanking you in advance yours sincerely, Uday. -- 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] NVT equilibration of DMSO solvent (Charmm all-atom force field)
On 21/06/2011 2:44 AM, udaya kiran marelli wrote: Dear GROMACS users, I have generated a 4*4*4 octahedral DMSO box containing 64 molecules (Charmm all-atom force field) which need to be NVT equilibrated in order to pass it for usage in genbox. Could one of you provide info on how to do the NVT and periodic boundary equilibration to remove the residual ordering of the solvent? Most tutorials will cover the details of such stages well. 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
