[gmx-users] How to recover the corrupted .xtc file?

Dear users, I have a corrupted .xtc file. I can read only part of the whole frame in VMD. When I gmx check the .edr file, there is no problem with 5001 frames. However if I do gmx check the .xtc file, then I get only 2954 frames out of 50001 frames. I used Gromacs 2019.6 with CUDA on a single no

Re: [gmx-users] Is Gromos force fields not recommended?

mended? > > It is not like that...gromos is not compatible with gromacs... decission > need to be taken depending on what system you want to simulate and what you > are expecting from the simulation. > On Tue 18 Feb, 2020, 6:27 AM Myunggi Yi, wrote: > > > Dear users, >

[gmx-users] Is Gromos force fields not recommended?

Dear users, As the same as the title, Are Gromos force fields not recommended in Gromacs? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

Re: [gmx-users] Hydrogen bonding criteria in Gromacs

Thu, Jan 16, 2020 at 8:20 PM Justin Lemkul wrote: > > > On 1/15/20 10:05 PM, Myunggi Yi wrote: > > Dear Dr. Justin Lemkul, > > > > Can you explain why the D-H-A is 150? > > > > If H-D-A is 30, then D-H-A should be smaller than 150 degrees. > > Since th

Re: [gmx-users] Hydrogen bonding criteria in Gromacs

Dear Dr. Justin Lemkul, Can you explain why the D-H-A is 150? If H-D-A is 30, then D-H-A should be smaller than 150 degrees. Since the sum of interior angles of a triangle should be 180 degrees... See the following triangle. H D

Re: [gmx-users] [gmx-user] 300K vs 310K for molecular dynamic simulation

Dear Quin, Since the lab temperature is around 300K, people who want to reproduce some specific (in vitro) experiment results run simulation at 300K. What is your target? Experimental condition? body temperature? It's up to you. If your simulations show significantly different results by 10K dif

Re: [gmx-users] Drude force field

18, 2019 at 11:22 AM Justin Lemkul wrote: > On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi wrote: > > > Thank you Dr. Lemkel, > > > > I don't have ions in my simulation. It's a neutral system with a protein > in > > membrane bilayer with solvent. > >

Re: [gmx-users] Drude force field

> > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > > > > I want to run a simulation with a polarizable force field. > > > > How and where can I get Drude force field for the current version of > > Gromacs? > > Everything you need to know:

Re: [gmx-users] Drude force field

ns. Which one should I use? Or, it there a way to modify the force field format to use the current version of Gromacs?, Then I will modify the format. On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > &

Re: [gmx-users] Drude force field

Thank you. On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > > > > I want to run a simulation with a polarizable force field. > > > > How and where can I get Drude force field

[gmx-users] Drude force field

Dear users, I want to run a simulation with a polarizable force field. How and where can I get Drude force field for the current version of Gromacs? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

[gmx-users] Drude force field

Dear users, How or where can I get the Drude polarizable force field file for current Gromacs version? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mail

[gmx-users] Difference between NH2 in c-term and aminoacids

Dear users, I am modifying top files to prepare my own n- and c-termini. Can someone explain why charges in the NH2 residue in "aminoacids.n.tdb" file and "aminoacids.rtp" are different? Thank you in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/

Re: [gmx-users] Performance

ilárd > > > On Wed, Mar 28, 2018 at 7:10 PM, Myunggi Yi wrote: > > Does it work? > > > > https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl > > > > How about this? > > > > > > Myunggi Yi > > > > On Wed, Mar 28, 201

Re: [gmx-users] Performance

Thanks. I used the exactly same program (same installation and same environment variable). How come this error depends on the *.mdp file? I don't get it with typical simulations such as md with PME etc, but I get it with this Dry_Martini mdp file (using sd, reaction field etc.). Myung

Re: [gmx-users] Performance

Does it work? https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl How about this? Myunggi Yi On Wed, Mar 28, 2018 at 12:20 PM, Mark Abraham wrote: > Hi, > > Attachments can't be accepted on the list - please upload to a file sharing > service and sha

Re: [gmx-users] Performance

I see. I am trying again. ​ ves <https://drive.google.com/drive/folders/1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl> ​ Myunggi Yi (이명기, Ph. D.), Professor Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of Engineering Interdisciplinary Program of Biomedical Mechanical &

Re: [gmx-users] Performance

I am attaching the file. Thank you. Myunggi Yi On Wed, Mar 28, 2018 at 11:40 AM, Szilárd Páll wrote: > Again, please share the exact log files / description of inputs. What > does "bad performance" mean? > -- > Szilárd > > > On Wed, Mar 28, 2018 at 5:31 PM, My

[gmx-users] Performance

entation/Errors --- So I did run simulation with the following command. gmx mdrun -deffnm md -ntmpi 1 Now the performance is extremely bad. Since yesterday, the log file still reporting the first step's energy. 2. This is the second question. Why? Can anyone help? Myunggi

[gmx-users] mdrun on single node with GPU

well (option -ntmpi). For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can anyone help? Thank you for any help in advance. Myunggi Yi -- Gromacs Users ma

[gmx-users] Typo in dry_martini force field

FYI I found a typo in dry_martini_v2.1_lipids.itp ERROR 1 [file dry_martini_v2.1_lipids.itp, line 690]: Duplicate atom index (11) in angles If this is correct, then modify the line 690 11 11 12 2 ma_ccc to 10 11 12 2 ma_ccc Myunggi Yi -- Gromacs Users mailing list

Re: [gmx-users] extending simulations

t; Mark > > On Mon, Jan 29, 2018 at 3:37 PM Myunggi Yi wrote: > > > Thank you for your help. > > > > Then how can the simulation be continued without previous cpt file > > (information)? > > > > Or, should I use another way to extend the simulations? > &g

Re: [gmx-users] extending simulations

Thank you all. Have a great day. Myunggi On Mon, Jan 29, 2018 at 9:40 AM, Mark Abraham wrote: > Hi, > > See > http://manual.gromacs.org/documentation/2018-latest/user-guide/managing- > simulations.html#extending-a-tpr-file > > Mark > > On Mon, Jan 29, 2018 a

Re: [gmx-users] extending simulations

Thank you for your help. Then how can the simulation be continued without previous cpt file (information)? Or, should I use another way to extend the simulations? Myunggi On Mon, Jan 29, 2018 at 9:10 AM, Justin Lemkul wrote: > > > On 1/29/18 9:07 AM, Myunggi Yi wrote: > &

[gmx-users] extending simulations

Thank you for any help, in advance. Myunggi Yi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests v

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

Peter, (ignoring full precision) Are the thermostat and barostat computed by coordinates and velocities, in principle ? Myunggi Yi (이명기, Ph. D.), Professor Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of Engineering Interdisciplinary Program of Biomedical Mechanical

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

Peter, I see. Thank you for the correction. MY -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://m

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

1. In principle, MD can be restarted if there are coordinates and velocities on the snapshot. 2. Even if you don't have velocity, you can assign random velocity with the specific temperature. In this case, you lose continuity of simulation. Don't worry. If you run same simulation with the exactly