Re: [gmx-users] Regarding getting trajectories in gromacs..

- Message from Dilip H N -     Date: Tue, 4 Apr 2017 10:18:23 +0530     From: Dilip H N Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] Regarding getting trajectories in gromacs..       To:

[gmx-users] XYZ file and obgmx

Dear Gromacs users , I have a xyz file and I used OBGMX ( topology generator ) for that . Now I have itp and top file , but the problem is I want to change UFF forcefield ( that used by obgmx ) to gromacs forcefields like Amber03 . Can you please let me know how can i do that ? I am new in

[gmx-users] Regarding getting trajectories in gromacs..

Hello, I have ran a md simulation for nsteps = 500 ; 2 * 500 = 1 ps (10 ns) dt = 0.002 ; 1e+07 fs nstxout= 5000 ; save coordinates every 20.0 ps nstvout= 5000 ; save velocities every 20.0 ps nstenergy= 5000 ; save energies every 20.0 ps nstlog= 5000 ; update log file

[gmx-users] continuation with different dt values

Hi, I’m continuing a run and setting init-step as the total steps completed in the run i’m continuing from, if I change the dt for the continuation do I need to scale the steps previously taken? i.e going from dt = 1 to dt =2, completing 100 steps in the first sim, does init-step take the

Re: [gmx-users] System almost blowing up

>> Hi, >> >> I?m receiving a couple (~15) EM did not converge warnings as well as a few >> (~3) 1,4 interaction >> warnings during my run. It looks like it starts down the path to blowing up >> but recovers. Is this ?recovery? >> system dependent? Should I take these messages (even without

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 156, Issue 13

> Such a short dt and strict niter should not be necessary in practice. The > failure of SCF to converge/LINCS warnings is what we typically refer to as > polarization catastrophe, so your system is on the brink of instability. > This > is one of the inherent problems of SCF in polarizable

Re: [gmx-users] How to extend simulation?

Thank you. So if the below is correct, and it will run for 100 ns? convert-tpr -s previous.tpr -extend 10 -o next.tpr gmx mdrun -deffnm next -cpi previous.cpt -- Original -- From: "Justin Lemkul";; Date: Tue, Apr 4, 2017 02:12 AM To:

Re: [gmx-users] How to extend simulation?

On 4/3/17 2:07 PM, ZHANG Cheng wrote: (Following Justin's suggestion) Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use

Re: [gmx-users] How to extend simulation?

Hi, Back up your files and try it :-) You will see that mdrun refuses to append if you change -deffnm. So either don't append or don't change the name. Mark On Mon, Apr 3, 2017 at 8:09 PM ZHANG Cheng <272699...@qq.com> wrote: > (Following Justin's suggestion) > > > Dear Gromacs Researchers, >

[gmx-users] How to extend simulation?

(Following Justin's suggestion) Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for the

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

On 4/3/17 2:01 PM, Dan Gil wrote: Thank you Dr. Lemkul, I am trying to run grompp with the md integrator, but I am getting this error: "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used" Should I ignore this warning with the -maxwarn option and try

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

Thank you Dr. Lemkul, I am trying to run grompp with the md integrator, but I am getting this error: "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used" Should I ignore this warning with the -maxwarn option and try running it? I will see if I obtain

Re: [gmx-users] System almost blowing up

On 4/3/17 1:42 PM, Dayhoff, Guy wrote: Hi, I’m receiving a couple (~15) EM did not converge warnings as well as a few (~3) 1,4 interaction warnings during my run. It looks like it starts down the path to blowing up but recovers. Is this “recovery” system dependent? Should I take these

Re: [gmx-users] How to extend simulation by changing the mdp file?

On 4/3/17 1:41 PM, ZHANG Cheng wrote: Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for

[gmx-users] System almost blowing up

Hi, I’m receiving a couple (~15) EM did not converge warnings as well as a few (~3) 1,4 interaction warnings during my run. It looks like it starts down the path to blowing up but recovers. Is this “recovery” system dependent? Should I take these messages (even without the subsequent

[gmx-users] How to extend simulation by changing the mdp file?

Dear Gromacs Researchers, My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to extend it to 100 ns. As shown on http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Should I use the following two lines of code for the files in the same folder? grompp

Re: [gmx-users] wt% of the solvent

ISHRAT Thank you very much. On Sun, Apr 2, 2017 at 11:50 PM, ISHRAT JAHAN wrote: > Hi, > You have to calculate the number of alcohol and water molecules in the box > and use genbox command with -nmol option.In -nmol put number of alcohol > molecule and from the output of

Re: [gmx-users] Order in which gromacs calculates non-bonded parameters

Hi, Offhand, gen-pairs won't work without matching pairtypes, but nonbond_params will override anything that might have been looked up from pairtypes. Mark On Mon, Apr 3, 2017 at 2:39 PM Vries, de, H.W. < h.w.de.vrie...@student.rug.nl> wrote: > Dear all, > > I was wondering: what priority does

[gmx-users] Order in which gromacs calculates non-bonded parameters

Dear all, I was wondering: what priority does GROMACS use for comparing [nonbond_params], [pairtypes], and gen-pairs-based cross-terms? I.e., are pairtypes additive to gen-pairs, with nonbond_params overwriting any cross-term defined through cross-terms? The reason I am asking is that I am

Re: [gmx-users] Missing bond

Dear Justin, Thanks for your kind help! Best regards, Sudip On Mon, Apr 3, 2017 at 5:20 PM, Justin Lemkul wrote: > > > On 4/1/17 1:18 AM, Sudip Das wrote: > >> Dear All, >> >> While I am preparing my system topology with pdb2gmx for a system >> containing enzyme with 30

Re: [gmx-users] Protein ligand complex simulation

Hi, Look at your docking result before you use it for something else. (Same goes for any computed result from any software.) Mark On Mon, 3 Apr 2017 14:06 RAHUL SURESH wrote: > The ligand is out of protein in the very first frame of production run. > Then that should

Re: [gmx-users] Protein ligand complex simulation

On 4/3/17 8:05 AM, RAHUL SURESH wrote: The ligand is out of protein in the very first frame of production run. Then that should be my docking error.? It sounds like your starting configuration was prepared incorrectly (however you manipulated it to prepare the system) or this is a PBC

Re: [gmx-users] Protein ligand complex simulation

The ligand is out of protein in the very first frame of production run. Then that should be my docking error.? On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul wrote: > > > On 4/3/17 7:56 AM, RAHUL SURESH wrote: > > Dear Justin > > > > First I apologise for the error I had made in

Re: [gmx-users] Protein ligand complex simulation

On 4/3/17 7:56 AM, RAHUL SURESH wrote: Dear Justin First I apologise for the error I had made in my previous mail. It's during production. I have recentered it. The ligand is out of the protein. The ligand is not in position where I docked. Then watch the recentered trajectory to see what

Re: [gmx-users] Protein ligand complex simulation

Dear Justin First I apologise for the error I had made in my previous mail. It's during production. I have recentered it. The ligand is out of the protein. The ligand is not in position where I docked. On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul wrote: > > > On 4/1/17 8:59

Re: [gmx-users] Regarding structure conformation

On 4/3/17 2:23 AM, Vytautas Rakeviius wrote: MD can not simulate chemical reactions. What you can do prepare different forms with acpype and compare all in some way. External tools aren't even necessary. One just needs to select the proper termini with pdb2gmx. -Justin On

Re: [gmx-users] Protein ligand complex simulation

On 4/1/17 8:59 AM, RAHUL SURESH wrote: I followed the complex simulation tutorial. Minimisation for 2ns FYI there is no time during energy minimization, so you did not do "2 ns" of minimization. I used auto dock to dock ligand with protein. During simulation I find the ligand out of

Re: [gmx-users] Missing bond

On 4/1/17 1:18 AM, Sudip Das wrote: Dear All, While I am preparing my system topology with pdb2gmx for a system containing enzyme with 30 non-ionic surfactant molecules in water, I got 36 number of bonds per surfactant molecules, but actually it has 37 bonds (anyways, the number of angle,

Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

Hi, Some of those tools calculate distribution functions. Please start by looking at them and seeing if they seem suitable. Mark On Mon, Apr 3, 2017 at 11:59 AM ISHRAT JAHAN wrote: > sorry i did not get what you said... > actually i want to calculate distribution of water

Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

sorry i did not get what you said... actually i want to calculate distribution of water at various distance around backbone as done in paper "Regulation and aggregation of intrinsically disordered peptides" by Zachary A.Levine et.al. On Mon, Apr 3, 2017 at 1:54 PM, Mark Abraham

Re: [gmx-users] gromacs Query

Hi, If you ask for .trr output, you get it. Stop using non-zero nst*out mdp settings that you don't want. Mark On Mon, Apr 3, 2017 at 11:31 AM Aman Deep wrote: > sir, > > I have tried *nstxctout *but it still making trr file ... is there any > option to make only

Re: [gmx-users] gromacs Query

sir, I have tried *nstxctout *but it still making trr file ... is there any option to make only xtc file ??? On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham wrote: > Hi, > > See > http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_ > Volume > >

Re: [gmx-users] Energy Miinimization question

As you set smaller emtol you do better and longer minimization. So with 1000 you stop simulation way before polymer forms some rings. You can check video with VMD Chimera or something. On Saturday, April 1, 2017 8:25 PM, Mishelle Oña wrote: Hello everybody, I

Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

Hi, So, you want to make a selection according to a geometric criterion, which is what gmx select does. Mark On Mon, Apr 3, 2017 at 10:12 AM ISHRAT JAHAN wrote: > i want to calculate number of water molecule within given distance from > protein. > > > On Mon, Apr 3, 2017

Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

i want to calculate number of water molecule within given distance from protein. On Mon, Apr 3, 2017 at 1:20 PM, Mark Abraham wrote: > Hi, > > It's not clear to me what you actually want, or why trjorder is even a > possible tool for the job. Look at >

Re: [gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

Hi, It's not clear to me what you actually want, or why trjorder is even a possible tool for the job. Look at http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html and find something useful. Mark On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN wrote: >

[gmx-users] Fwd: analysis of osmolyte at particular distance from backbone

-- Forwarded message -- From: ISHRAT JAHAN Date: Fri, Mar 31, 2017 at 12:51 PM Subject: analysis of osmolyte at particular distance from backbone To: gmx-us...@gromacs.org Dear all, I want to calculate the number of osmolyte molecule at particular distance

Re: [gmx-users] Fwd: Dipole moment of water

Hi, I imagine it does whatever is standard, e.g. from negative to positive. What does it report for a single water molecule? Mark On Mon, Apr 3, 2017 at 8:24 AM Alex wrote: > No comment on below question, please? > > Regards, > Alex > > -- Forwarded message

Re: [gmx-users] gromacs Query

Hi, See http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark On Mon, Apr 3, 2017 at 9:27 AM Aman Deep wrote: > sir is there any way to create only XTC file from mdrun only. the server on > which I am working is not providing enough

[gmx-users] gromacs Query

sir is there any way to create only XTC file from mdrun only. the server on which I am working is not providing enough space and my trr file is too much large. thank you -- Aman Deep MSc Bioinformatics Jamia Millia Islamia New Delhi - 110025 -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Regarding structure conformation

MD can not simulate chemical reactions. What you can do prepare different forms with acpype and compare all in some way. On Monday, April 3, 2017 6:51 AM, Dilip H N wrote: Hello, I have a non zwitterionic glycine molecule, and have solvated it with water,

[gmx-users] Fwd: Dipole moment of water

No comment on below question, please? Regards, Alex -- Forwarded message -- From: Alex Date: Wed, Mar 29, 2017 at 2:27 PM Subject: Dipole moment of water To: gmx-us...@gromacs.org Dear gromacs user, What is the direction of the water's dipole moment