[gmx-users] Rerun a period of trajectory with more frequent output.

Hi I have completed a protein-ligand MD simulation using Gromacs v4.5.5 and found protein undergoes a large conformational change. But sampling is too sparse to get intermediate states. In order to get some intermediate states I have to rerun the confromational change period of trajectory with more

Re: [gmx-users] extending simulation

Maybe you can dump the frame at t=50 ns using "gmx trjconv" and use "gmx grompp" to do an extending simulation when you don't have a .cpt file. Of course this is not an exact continuation. On 10 August 2016 at 20:04, sun.iba2 wrote: > You must have provided 5 for -extend flag in convert-tpr.

Re: [gmx-users] output file format under pbc

Hi, I can't find your figures and I guess this link may be helpful to you: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions On 26 August 2016 at 09:49, Chang Woon Jang wrote: > Dear Gromacs Users, > > Sorry for the misspelling of "Grimaces Users" due to automatic

[gmx-users] GB parameter(s) missing or negative for atom type 'xxx'.

Hi, I want to simulate a protein-ligand complex with implicit solvent. After I ran "grompp" command it prompted me there were some missing GB parameters. I guess the problem is that some atom types in my system are not included in the gbsa.itp file. If it is the case, do you know where can I find t

Re: [gmx-users] topology build

Hi, Have a look at this tutorial, and I hope this helps. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/ On 28 August 2016 at 02:05, Nikhil Maroli wrote: > Did you want to make topology for the ligand? > There are already some tools available for that, try those o

[gmx-users] Is Generalized Born implicit solvent model faster than explicit solvent model?

Hi everyone, I did two reMD simulations with GB implicit solvent and TIP3P solvent using Gromacs4.5.5 respectively (1 cpu per replica for both of them). My results show that implicit solvent model is not faster than explicit solvent model. I'm confused why the implict solvent model is so slow? Or s

[gmx-users] Is Generalized Born implicit solvent model faster than explicit solvent model?

Hi everyone, I did two reMD simulations with GB implicit solvent and TIP3P solvent using Gromacs4.5.5 respectively (1 cpu per replica for both of them). My results show that implicit solvent model is not faster than explicit solvent model. I'm confused why the implict solvent model is so slow? Or s

[gmx-users] Including TIP3P water molecules in GB model.

Hi, I think some crystal water molecules are important to my the system. Can I keep the crystal water molecules when I run a MD simulation with implicit water model? Thank you in advance! Best regards! Dading Huang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.

[gmx-users] parameters of GppNHp

Hi everyone, I want to simulate a protein-ligand complex. The ligand is a GppNHp molecule and an analogue of GTP. I cannot find parameters of GppNHp in AMBER parameter database (parameters of GTP are supplied there). Can you tell me how to get the parameters of GppNHp? Thank you in advance! Dading

Re: [gmx-users] parameters of GppNHp

I'm using AMBER force field. On 18 September 2016 at 15:37, Dd H wrote: > Hi everyone, > I want to simulate a protein-ligand complex. The ligand is a GppNHp > molecule and an analogue of GTP. I cannot find parameters of GppNHp in > AMBER parameter database (parameters of GTP a

Re: [gmx-users] parameters of GppNHp

Thank you. I have found a tutorial and I will try to derive them. On 19 September 2016 at 00:40, Justin Lemkul wrote: > > > On 9/18/16 3:37 AM, Dd H wrote: > >> Hi everyone, >> I want to simulate a protein-ligand complex. The ligand is a GppNHp >> molecule and an

Re: [gmx-users] parameters of GppNHp

topology and coordinate file >> for the same please share the details >> >> Thanks in advance >> Anu George >> >> - Original Message - >> From: "Dd H" >> To: gmx-us...@gromacs.org >> Sent: Monday, September 19, 2016 6:59:01 AM >> Sub

Re: [gmx-users] parameters of GppNHp

2 -ek > > grms_tol=0.005 > > > > Please suggest a way to overcome this error" > > Thanks in advance > > Anu George > > > > - Original Message - > > From: "Dd H" > > To: gmx-us...@gromacs.org > > Sent: Wednesday, September 21,

[gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Hi everyone, I generated a .top file of a ligand using acpype for MD simulations. There are some new atom types in [ atomtypes ] section, but the data of mass and charge columns of the section are zeros. However they can be found in the [ atoms ] section. Can you tell me if this file is ok for MD s

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

amber and calculate partial charges. See > acpype -h > > On 12 October 2016 at 09:56, Dd H wrote: > > > Hi everyone, > > I generated a .top file of a ligand using acpype for MD simulations. > There > > are some new atom types in [ atomtypes ] section, but the da

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Thank you! On 12 October 2016 at 19:50, Alan wrote: > It's all fine. > > On 12 October 2016 at 12:34, Dd H wrote: > > > I use this command: > > acpype -p filename.prmtop -x filename.inpcrd > > > > It generates parameter files for GROMACS and my questio

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

changed here too.* So does it means the mass and charge of [ atomtypes ] section could be modified in [ atoms ] section? On 12 October 2016 at 23:30, Alan wrote: > But read the GMX manual to understand why it's all fine. > > On 12 October 2016 at 13:29, Dd H wrote: > > > T

Re: [gmx-users] Fwd: Questions for the forum

You can reduce your box size to get a smaller system. On 13 October 2016 at 17:41, Matilde Viegas wrote: > Hi, > > my name is Matilde. This is my first time using GROMACS. I'm switching from > AMBER to GROMACS however I'm having some trouble reproducing my system: > > In AMBER, I'm working with

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Thank you so much! On 13 October 2016 at 20:07, Justin Lemkul wrote: > > > On 10/12/16 11:06 PM, Dd H wrote: > >> I found these words in the GROMACS v4.5.5 manual: >> >> *[ atoms ] : defines the molecule, where nr and type are fixed, the rest >> is >>

Re: [gmx-users] how to find energy barrier between two cluster centroids?

I think the Free Energy Landscape (FEL) is what you are looking for. Dading Huang On 8 November 2016 at 13:42, Seera Suryanarayana wrote: > Dear gromacs users, > > I have done 100ns simulation for a peptide with 50 residues length and > I generated clusters. Now I would like to calculate the en

Re: [gmx-users] (no subject)

If your residue contains new atom types, you should add them to the atomtypes.atp and ffnonbonded.itp files. Dading Huang On 8 November 2016 at 11:44, Kingsley Theras Primus Dass . < 105726...@gms.tcu.edu.tw> wrote: > Hello users!! > > I generated a Topology file for SO3- using ATB topology gene

Re: [gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

Exchange their atom names？ Dading Huang On Wed, Nov 9, 2016 at 7:23 PM, Dawid das wrote: > Dear Gromacs Experts, > > I know how to specify which Glu/Asp residues are to be > protonated/deprotonated with > pdb2gmx tool. However, I do not like that the hydrogen is added to one of > the oxygen ato

Re: [gmx-users] (no subject)

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Have a look at this, hope it's helpful. Dading Huang On Sat, Nov 19, 2016 at 1:36 PM, Kingsley Theras Primus Dass . < 105726...@gms.tcu.edu.tw> wrote: > Dear Users!! > > > I have a question about RMSD. I ran MＤ simu

Re: [gmx-users] How to read .dat file

I think this link should be helpful. http://manual.gromacs.org/programs/gmx-rms.html You can have a look at rms.xvg file, it contains rmsd values. Best regards, Dading Huang On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv wrote: > I generated a .dat file with the following command: > gmx rms -s .