Re: [gmx-users] affect of water removal on subsequent energy calculations

For an additive force field, the two numbers are in agreement, E_tot - E_13 - E_23 - E_33 = E_12, by definition. You can easily design a test case that will prove this. I know. I have it in front of me. ;) The dielectric constant of the medium is not included in the calculation, at least not

Re: [gmx-users] affect of water removal on subsequent energy calculations

On 4/11/18 3:09 PM, Alex wrote: Mark, Justin: This is two against one, even though noone was questioning the additivity of energy in forcefields with constant charges, etc. So, let's go back specifically to solvation. Consider a system with two oppositely charged ions (1 and 2) in water

Re: [gmx-users] affect of water removal on subsequent energy calculations

Mark, Justin: This is two against one, even though noone was questioning the additivity of energy in forcefields with constant charges, etc. So, let's go back specifically to solvation. Consider a system with two oppositely charged ions (1 and 2) in water of your choosing (group 3). For

Re: [gmx-users] RMSF started increasing after 60 ns simulation

On 4/11/18 11:17 AM, MD wrote: Hi Justin, Another quick question. When we talk about more independent runs, did you mean a run with another force field or just simply repeating the run? Depends on what you're trying to prove. If you want to demonstrate that your results are not an artifact

[gmx-users] Triclinic box of solvent

Hello, I am trying to add solvent to both sides of a triclinic crystal. I used editconf to create a triclinic box and placed my crystal in the center of the box. After that I used gmx solvate to add solvent to the remaining parts of the box. Upon visualization of the .gro file I noticed that

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Hi Justin, Another quick question. When we talk about more independent runs, did you mean a run with another force field or just simply repeating the run? Thanks, Ming On Wed, Apr 11, 2018 at 10:52 AM, MD wrote: > Thank you. > Ming > > > On Wed, Apr 11, 2018 at 10:46 AM,

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Thank you. Ming On Wed, Apr 11, 2018 at 10:46 AM, Justin Lemkul wrote: > > > On 4/11/18 10:44 AM, MD wrote: > >> Thank you Justin :) >> I wonder what is your strategy when considering what criteria could be >> used >> for determining convergence of the simulation? >> > > If

Re: [gmx-users] RMSF started increasing after 60 ns simulation

On 4/11/18 10:44 AM, MD wrote: Thank you Justin :) I wonder what is your strategy when considering what criteria could be used for determining convergence of the simulation? If all the relevant quantities that I care about are invariant over time based on error estimates, it's converged.

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Thank you Justin :) I wonder what is your strategy when considering what criteria could be used for determining convergence of the simulation? Ming On Wed, Apr 11, 2018 at 10:30 AM, Justin Lemkul wrote: > > > On 4/11/18 10:26 AM, MD wrote: > >> Thank you Justin. Two quick

Re: [gmx-users] RMSF started increasing after 60 ns simulation

On 4/11/18 10:26 AM, MD wrote: Thank you Justin. Two quick questions (learning questions :)) 1. How do I apply several invocations of trjconv, (a quick guide would be appreciated) http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow If I

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Thank you Justin. Two quick questions (learning questions :)) 1. How do I apply several invocations of trjconv, (a quick guide would be appreciated) 2. Several literature used only 90-100 ns time window for RMSF analysis in a 100ns run. Does that mean the later the time window is the more value of

Re: [gmx-users] Criteria used to get DIHEDRAL DISTRIBUTION at discrete points

On 4/11/18 10:17 AM, sanjeet kumar singh ch16d012 wrote: Hello List, I wanted to know that when we calculate dihedral distribution in GROMACS using gmx angle, it gives us values at discrete points like -180,-179 etc then what happens to the angles that falls in between -180 and -179?

Re: [gmx-users] RMSF started increasing after 60 ns simulation

On 4/11/18 10:16 AM, MD wrote: Hi, I wouldn't do cherry-picking. I am just confused how I can trust the data if the RMSD goes crazy in that range? Also based on the command I used I think the PBC has been taken care of, please correct me if I am wrong :) And It would be very interesting, if

[gmx-users] Criteria used to get DIHEDRAL DISTRIBUTION at discrete points

Hello List, I wanted to know that when we calculate dihedral distribution in GROMACS using gmx angle, it gives us values at discrete points like -180,-179 etc then what happens to the angles that falls in between -180 and -179? And what criteria is used to decide that a value lying in

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Hi, I wouldn't do cherry-picking. I am just confused how I can trust the data if the RMSD goes crazy in that range? Also based on the command I used I think the PBC has been taken care of, please correct me if I am wrong :) And It would be very interesting, if the RMSF of wild type started

Re: [gmx-users] RMSF started increasing after 60 ns simulation

On 4/11/18 10:04 AM, MD wrote: Hi, Yes I am comparing the trajectories side by side and I ran a RMSD of wild type too. I looked at the RMSD of wild type and it looks like it became unstable after 70ns. In this case the only approach is to compare the trajectories in time windows before 70ns.

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Hi, Yes I am comparing the trajectories side by side and I ran a RMSD of wild type too. I looked at the RMSD of wild type and it looks like it became unstable after 70ns. In this case the only approach is to compare the trajectories in time windows before 70ns. Would that be right? Thank you, MD

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Hi Mark, I found some of the regions are more flexible in the mutant in several time windows but not in the others. Should I trust the later time windows than the former ones? Thanks, MD On Wed, Apr 11, 2018 at 9:23 AM, Mark Abraham wrote: > Hi, > > What did you

Re: [gmx-users] RMSF started increasing after 60 ns simulation

On 4/11/18 9:41 AM, MD wrote: Hi Justin, This was the command I used for both wild type and mutant. I wonder if you could think of any reason that made only the wild type have the PBC effects? gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -ur compact Visualize each trajectory as

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Hi Justin, This was the command I used for both wild type and mutant. I wonder if you could think of any reason that made only the wild type have the PBC effects? gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -ur compact Thank you, MD On Wed, Apr 11, 2018 at 9:23 AM, Justin Lemkul

Re: [gmx-users] RMSF started increasing after 60 ns simulation

Hi, What did you learn from viewing the trajectory in a visualization tool? Mark On Wed, Apr 11, 2018 at 3:22 PM MD wrote: > Hi Gromacs folks, > > I was trying to use RMSF to compare c-alpha of a wild type and mutant in a > 100 ns simulation. I discarded the 10-30 ns and

Re: [gmx-users] RMSF started increasing after 60 ns simulation

On 4/11/18 9:22 AM, MD wrote: Hi Gromacs folks, I was trying to use RMSF to compare c-alpha of a wild type and mutant in a 100 ns simulation. I discarded the 10-30 ns and compared them side by side in non-overlapping time windows of 30-40ns, 40-50ns, 50-60ns, 60-70 ns, 70-80 ns, 80-90 ns and

[gmx-users] RMSF started increasing after 60 ns simulation

Hi Gromacs folks, I was trying to use RMSF to compare c-alpha of a wild type and mutant in a 100 ns simulation. I discarded the 10-30 ns and compared them side by side in non-overlapping time windows of 30-40ns, 40-50ns, 50-60ns, 60-70 ns, 70-80 ns, 80-90 ns and 90-100ns. The RMSF of wild type

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

You can use either gmx trjorder with the nshell parameter (if it is as simple as within Xnm of Y, use nshell parameter, see manual) or gmx select (if you need some more complex selection). On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N wrote: > Hello all, > > I want to

Re: [gmx-users] OPLS3 forcefield

I use and recommend the project STaGE (OPLS-AA and other forcefields): https://gerrit.gromacs.org/#/admin/projects/STaGE Best regards, Krzysztof 2018-04-07 23:04 GMT+02:00 Alex : > Not sure about OPLS3, but for the publicly available OPLS-AA there are > many resources,

Re: [gmx-users] bug in trjconv?

BS”D Dear Mark, did the .tpr actually match the trajectory file? Sorry, that was indeed the problem (mismatch of -f and -s files). Thanks for the hint Harry Harry M. Greenblatt Associate Staff Scientist Dept of

Re: [gmx-users] Freezing atoms, energy group exclusion and pressure calculation

Hi, This combination is only available with the group scheme at this time, unfortunately. Probably it will work in the 2019 version. Mark On Tue, Apr 10, 2018 at 2:00 PM Mateusz Bieniek wrote: > I am simulating metallic surface together with proteins and I need to use >

Re: [gmx-users] affect of water removal on subsequent energy calculations

Hi, What Justin said, plus the observation that you should know how you plan to analyze the results before you run the simulation. In this case, that means knowing what you'll learn from rerun energies. Sometimes this means that you won't ever run the simulations, and those are the really

Re: [gmx-users] bug in trjconv?

Hi, It's hard to say whether there's a bug, given this information. What version of GROMACS was it, were there any warnings on the terminal output, did the .tpr actually match the trajectory file? Mark On Wed, Apr 11, 2018 at 1:14 PM Harry Mark Greenblatt < harry.greenbl...@weizmann.ac.il>

Re: [gmx-users] bug in trjconv?

On 4/11/18 7:13 AM, Harry Mark Greenblatt wrote: BS”D In a given system with several chains, after minimisation the chains are split up by PBC. Using trjconv on this file to put all the chains back into a unified complex, the Ions are converted to water molecules. The input file (-f)

Re: [gmx-users] affect of water removal on subsequent energy calculations

On 4/11/18 4:21 AM, Alex wrote: Screening effects in Gromacs come in a rather non-straightforward manner in terms of data extraction: they certainly exist within the simulations in the form of the fields induced by local water orientation, but to extract them from reruns is extremely

[gmx-users] bug in trjconv?

BS”D In a given system with several chains, after minimisation the chains are split up by PBC. Using trjconv on this file to put all the chains back into a unified complex, the Ions are converted to water molecules. The input file (-f) and the reference file (-s) had waters and Ions

Re: [gmx-users] g_sans calculation

Hi! Details of implementation described here doi:10.1134/S1027451013060372 Cryson doesnt do time averaging. However for sinlge frame it shows same results as g_sans João Henriques писал 23-02-2018 23:48: I understand your pain, and the same could be said about gmx saxs as well. As Micholas

Re: [gmx-users] affect of water removal on subsequent energy calculations

BS”D Ok, thanks for the advice, Harry On 11 Apr 2018, at 11:21 AM, Alex > wrote: Screening effects in Gromacs come in a rather non-straightforward manner in terms of data extraction: they certainly exist within the simulations in the form of

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

gmx select On Wed, Apr 11, 2018 at 9:54 AM, Dilip.H.N wrote: > Hello all, > > I want to get the water molecules which are at a certain distance (say all > the water molecules which are within 0.35nm of the Nitrogen atom of glycine > molecule). How can i get this all

Re: [gmx-users] affect of water removal on subsequent energy calculations

Screening effects in Gromacs come in a rather non-straightforward manner in terms of data extraction: they certainly exist within the simulations in the form of the fields induced by local water orientation, but to extract them from reruns is extremely challenging even if you're outputting

Re: [gmx-users] affect of water removal on subsequent energy calculations

BS”D Dear Alex, Not *explicitly* related to water: we would like to look at interaction energies between parts of proteins, or proteins and DNA. So screening comes to mind… Harry On 11 Apr 2018, at 10:51 AM, Alex > wrote: If you plan

[gmx-users] Regarding getting the coordinates within certain region of amino-acid

Hello all, I want to get the water molecules which are at a certain distance (say all the water molecules which are within 0.35nm of the Nitrogen atom of glycine molecule). How can i get this all the coordinates.? Any specific commands..?? Thank you. --- With Best Regards, Dilip.H.N PhD

Re: [gmx-users] affect of water removal on subsequent energy calculations

If you plan to extract anything explicitly related to water from your reruns -- very much so. Basically unusable trajectories. Alex On 4/11/2018 1:48 AM, Harry Mark Greenblatt wrote: B”SD In an effort to reduce the size of output xtc files of simulations of large systems, we thought of

[gmx-users] affect of water removal on subsequent energy calculations

B”SD In an effort to reduce the size of output xtc files of simulations of large systems, we thought of saving these files without water molecules. It occurred to us, however, that upon subsequent cpu-only reruns in order to do energy calculations, these results would be adversely affected,

Re: [gmx-users] Protein atomic charges modeling question

Since molecular dynamics simulations are classical in nature, you, or the forcefield you choose, must set the partial atomic charges. You must also determine your desired protonation states based on the pH conditions you want to simulate. To actually answer your question, there are programs that