[gmx-users] DSSP installation

  Hii all I want to calculate the number of helical contain of protein. For that I tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the tar file and extracted it. Then place the dssp fiolder in /usr/local/bin and exported the path to ./bashrc file export DSSP=/usr/local/bin/ds

Re: [gmx-users] DSSP installation

- Message from João Henriques -     Date: Sat, 9 Dec 2017 11:29:41 +0100     From: João Henriques Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] DSSP installation       To: gmx-us...@gromacs.org The output is telling you what is wrong. Gromacs doesn't support version 3.

Re: [gmx-users] DSSP installation

- Message from João Henriques -     Date: Sat, 9 Dec 2017 11:29:41 +0100     From: João Henriques Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] DSSP installation       To: gmx-us...@gromacs.org The output is telling you what is wrong. Gromacs doesn't support version 3.

[gmx-users] Umbrella sampling

Hi all I am doing umbrella sampling taking distance between COM as a reaction coordinate. when I am trying to calculate PMF using the following command  gmx wham -it tpr-files.dat -if pullf-files.dat  -o free.xvg -hist hist.xvg I got an error  Program:     gmx wham, version 2016.3 Source file:

Re: [gmx-users] Umbrella sampling

- Message from Dhaniram Mahato -     Date: Tue, 19 Dec 2017 21:30:05 +0800     From: Dhaniram Mahato Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling       To: gmx-us...@gromacs.org Hi, There could be format problem. You can create your own .dat files by

Re: [gmx-users] Umbrella sampling

- Message from Dhaniram Mahato -     Date: Tue, 19 Dec 2017 21:30:05 +0800     From: Dhaniram Mahato Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling       To: gmx-us...@gromacs.org Hi, There could be format problem. You can create your own .dat files by

Re: [gmx-users] Umbrella sampling

- Message from "Jefferies D.F." -     Date: Tue, 19 Dec 2017 20:56:34 +     From: "Jefferies D.F." Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling       To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se Out of curiosity, how did yo

Re: [gmx-users] Umbrella sampling

- Message from Mark Abraham -     Date: Fri, 22 Dec 2017 00:42:31 +     From: Mark Abraham Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling       To: gmx-us...@gromacs.org       Cc: gromacs.org_gmx-users@maillist.sys.kth.se Hi, Yes, the parsing of th

[gmx-users] topology file error

Hii all I have prepared the topology file for urea molecule in AMBER99sb-ildn force field taking the parameters from ffbonded.itp and  ffnonbonded.itp available in AMBER folder. After simulation the urea molecule is somewhat distorted. The N-H bond is tilted. Please suggest me how to solve this pr

[gmx-users] segmentation fault

Hii all I am trying to simulate biomolecule in Guanidinium chloride in AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in energy minimization step but in NVT step files are generated and shows segmentation

[gmx-users] segmentation fault

Hii all I am trying to simulate biomolecule in Guanidinium chloride in AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in energy minimization step but in NVT step files are generated and shows segmentation

[gmx-users] DNA strands are separated

Hii all I am trying to do DNA simulation in water. I have done 200ns mdrun for that. When I am trying to see the snapshot of different frames in VMD, it shows that DNA strands are separated and one strand is out of the box. So I couldn't get the picture of different frames with actual solvent orie

[gmx-users] Fwd: DNA strands are separated

--- Begin Message --- Hii all I am trying to do DNA simulation in water. I have done 200ns mdrun for that. When I am trying to see the snapshot of different frames in VMD, it shows that DNA strands are separated and one strand is out of the box. So I couldn't get the picture of different frames

Re: [gmx-users] DNA strands are separated

- Message from Peter Stern -     Date: Tue, 24 Apr 2018 07:36:48 +     From: Peter Stern Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] DNA strands are separated       To: "'gmx-us...@gromacs.org'" Hi, This is probably just a periodic boundary issue.  Use gmx trjco

[gmx-users] % of H-bond occupancy

Hii I want to calculate % of H-bond occupancy between DNA base pair atoms and Urea molecule in gromacs. Is it possible to do this in gromacs? If not then what is the way to do that? Thanks Sunipa  -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailin

[gmx-users] Groove width

Hi all I am doing simulation of DNA molecule. I want to calculate groove width of DNA in GROMACS. How to do this? Someone please help. Thanks Sunipa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Groove width

  Thank you for your suggestion. This is a new thing I am learning. -- 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 req

Re: [gmx-users] Groove width

Hii David     I want to see if there is any change in the groove width in presence of different solvents. I thing this can give me some information of DNA structural change if it is happening in that particular solvent. -- Gromacs Users mailing list * Please search the archive at http://www.gro

[gmx-users] Centering the molecule

Hi all I want to center my molecule into a rectangular box by GROMACS. I am using the following command: gmx trjconv -f  traj.trr -s md.tpr -center -pbc  mol -b 100 -e 120 -o  test.gro  But output  shown is still out of the box. This command works for cubic box. Is there anything different flag fo

[gmx-users] Fwd: Centering a molecule

Hi all I want to center my molecule into a rectangular box after final mdrun by GROMACS. I am using the following command: gmx trjconv -f  traj.trr -s md.tpr -center -pbc  mol -b 100 -e 120 -o  test.gro  But output  shown is still out of the box. This command works for cubic box. Is there anything

Re: [gmx-users] Groove width

Hii I have tried installation of do_x3dna in ubuntu system following the instructions given in the link. Installation done successfully then I have written the path of do_x3dna in .bashrc file(export do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc. Then I tried doing do_x3d

Re: [gmx-users] Groove width

- Message from rajendra kumar -     Date: Mon, 4 Jun 2018 12:23:56 +0200     From: rajendra kumar Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Groove width       To: Discussion list for GROMACS users I am doing simulation of DNA molecule. I want to calculate groove wi

Re: [gmx-users] Groove width

Hii Thank you for your help. It is working successfully. Sunipa -- 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 request

[gmx-users] g_mmpbsa

Hii all I want to calculate the binding energy between a biomolecule and ligand. I have tried installing  g_mmpbsa but  my gromacs version is 2016.3. Can I use g_mmpbsa with gromacs-2016.3 or any other way to calculate the binding energy?  Thanks Sunipa -- Gromacs Users mailing list * Please sear

[gmx-users] electrostatic and LJ energy

Hi all I want to calculate the electrostatic and LJ energy between a part of DNA and ligand system in GROMACS-2016.3. How to do this? Example: Phosphate - ligand electrostatic and LJ energy thanks Sunipa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/

Re: [gmx-users] how to restart a job in grmacs

- Message from SHAHEE ISLAM -     Date: Thu, 27 Dec 2018 16:16:18 +0530     From: SHAHEE ISLAM Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] how to restart a job in grmacs       To: gmx-us...@gromacs.org hi, i have run a simulation for 10 ns but after 4 ns due to power off

Re: [gmx-users] how to restart a job in grmacs

- Message from SHAHEE ISLAM -     Date: Thu, 27 Dec 2018 16:41:21 +0530     From: SHAHEE ISLAM Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to restart a job in grmacs       To: gmx-us...@gromacs.org thank you so much for your reply. -extend 5000 what does it signif

Re: [gmx-users] how to restart a job in grmacs

- Message from SHAHEE ISLAM -     Date: Thu, 27 Dec 2018 16:52:17 +0530     From: SHAHEE ISLAM Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to restart a job in grmacs       To: gmx-us...@gromacs.org thank you is the trajectory wil be from 0-15 ns or it will be from

Re: [gmx-users] electrostatic and LJ energy

- Message from Dr Tushar Ranjan Moharana -     Date: Thu, 27 Dec 2018 17:01:10 +0530     From: Dr Tushar Ranjan Moharana Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] electrostatic and LJ energy       To: gromacs.org_gmx-users@maillist.sys.kth.se You can use gmx energy (g_e

[gmx-users] amber99parmbsc1 force field

Hii all I want to use Amber99 parm bsc1 force field to simulate nucleic acid system in GROMACS 2016.3. For that I have downloaded  amber99bsc1.ff and copy the folder to gromacs software. Is this right way? Please suggest something. Is this the right force field for nucleic acids? I am attaching th

[gmx-users] water mediated Hbond

Dear all I want to determine the water mediated hydrogen between DNA bases and small molecule. What extra flag should I use in gmx hbond command? Is there any other option to capture the water mediated Hbonds? Please suggest something. Sunipa Sarkar -- Gromacs Users mailing list * Please s

[gmx-users] gmx hbond query

Dear all I want to determine the water mediated hydrogen between DNA bases and small molecule. What extra flag should I use in gmx hbond command? Is there any other option to capture the water mediated Hbonds? Please suggest something. Sunipa Sarkar -- Gromacs Users mailing list * Please s

Re: [gmx-users] water mediated Hbond

Hii Thank you for your reply. So as u suggest I have to calculate 2 Hbond separately. But for how long that water mediated Hbond is stable; for that can I use Hbond number with time? For how many frames both the bonds appearing together. Is this right? One more thing is that I want to cal

Re: [gmx-users] water mediated Hbond

Hi Then what is the write way to calculate lifetime of a Hbond from gromacs? - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -     Date: Mon, 13 May 2019 22:24:51 +0530     From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> Reply-To: gmx-us...@gromacs.org Subject: Re:

Re: [gmx-users] water mediated Hbond

Then what is the right way to calculate lifetime of a hydrogen bond? - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -     Date: Mon, 13 May 2019 22:24:51 +0530     From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-use

Re: [gmx-users] water mediated Hbond

Hi In gmx hbond command there is a flag -ac -contact which gives hbond autocorrelation function with respect to time. Can I use that to get idea about lifetime of a Hbond? Because integration of the autocorrelation function will give the lifetime. Is there anything wrong? - Message

Re: [gmx-users] water mediated Hbond

Thank you for your kind reply. - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -     Date: Fri, 17 May 2019 13:33:30 +0530     From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] water mediated Hbond       To: gmx

Re: [gmx-users] ENERGY MINIMISATION

Hii I think this is due to the periodic boundary condition. Once you try to cut the .gro file using -pbc mol by gmx trjconv command. Hope this will work otherwise it is your system error, you need to modify your molecule topology file. - Message from Dhrubajyoti Maji -     Dat

[gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

- Forwarded message from sp...@iacs.res.in -    Date: Fri, 24 Mar 2017 16:24:21 +0530    From: sp...@iacs.res.in Subject: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?      To: gmx-us...@gromacs.org Hello, I am a new user of gromacs. I am tryi

[gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

--- Begin Message --- Hello, I am a new user of gromacs. I am trying to calculate SASA for a protein system. I have used the command gmx sasa -f traj.trr -s md.tpr -o sasa.xvg -n index.ndx From this I can only get the total SASA but I want hydrophobic and hydrophilic SASA separately. I know

Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

- Message from Mark Abraham -     Date: Tue, 28 Mar 2017 12:04:42 +     From: Mark Abraham Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?       To: gmx-us...@gromacs.org H

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: gromacs.org_gmx-users@maillist.sys.kth.se Hello, I have ran a md simulation for nsteps

Re: [gmx-users] how to know solvent molecule number

- Message from Chintan Bhagat -     Date: Wed, 5 Apr 2017 18:42:30 +0530     From: Chintan Bhagat Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] how to know solvent molecule number       To: gromacs.org_gmx-users@maillist.sys.kth.se Hello, I want to do stimulation of my pro

[gmx-users] Protein goes out of the box

Hii all, I have simulated protein in 45% ethanol water mixture for 100ns. After completion of the job I saw that maximum portion of my protein goes out of the box. Then I have done trjconv -pbc mol to the trajectory file. After trjconv some portion of the protein is still out of the box. I want to

Re: [gmx-users] Protein goes out of the box

- Message from Justin Lemkul -     Date: Tue, 25 Apr 2017 10:40:40 -0400     From: Justin Lemkul Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein goes out of the box       To: gmx-us...@gromacs.org On 4/25/17 10:35 AM, sp...@iacs.res.in wrote: Hii all, I have simu

Re: [gmx-users] RDF Values

I think you can use -cut 0 -rmax 1.5 this will give you the RDF upto 1.5 nm.- Message from "Pandya, Akash" -     Date: Mon, 31 Jul 2017 07:29:19 +     From: "Pandya, Akash" Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] RDF Values       To: gmx-us...@gromacs.org Hi all,

[gmx-users] problem installing plumed-2.3.2

Hii all    I am trying to install plumed-2.3.2 in CRAY system. I am using this command to configure plumed  ./configure --enable-mpi --prefix=/work/plumed-2.2.5/ At the end it shows a warning  configure: WARNING: PLUMED will NOT be compiled using MPI because MPI have not been found! configu

[gmx-users] umbrella sampling

Hi all I am trying to do umbrella sampling of protein with radius of gyration as reaction coordinate using gromacs-2016.3 patched with plumed-2.3.2. I have chosen 13 configurations of protein for sampling. Now I want to analyse the data. So how to plot histogram and PMF w.r.t radius of gyartion? C

[gmx-users] umbrella sampling

Hi all I am trying to do umbrella sampling of protein unfolding with radius of gyration as reaction coordinate using gromacs-2016.3 patched with plumed-2.3.2. I want to calculate free energy for the system. I am using the following command gmx wham P=1.4 1.5 100 0.001 300 0 metadata.dat  free.da

[gmx-users] Binary mixture

Hi all I want to prepare a  cubic box of 6M urea. How many molecules of urea and how many water molecules should be added to the simulation box? How to calculate these numbers? Please help me to solve this. Thanks Sunipa -- Gromacs Users mailing list * Please search the archive at http://www.gr

Re: [gmx-users] Binary mixture

- Message from Justin Lemkul -     Date: Fri, 15 Sep 2017 11:12:37 -0400     From: Justin Lemkul Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Binary mixture       To: gmx-us...@gromacs.org On 9/15/17 10:59 AM, sp...@iacs.res.in wrote: Hi all I want to prepare a  cubic

[gmx-users] Contact map

Hi all I want to generate a contact map for all the residues of lysozyme protein. I am using gmx mdmat to generate this. Can I generate a text file (which can be open in Grace) except the image files(eg: xpm file)? Please let me know the particular flag which I can use to get a *.xvg file. Thanks

[gmx-users] trajectory error

Dear all I have performed a 400 ns mdrun in GROMACS-2016.3. Due to some problem the job was stopped then I rerun the simulation using  state.cpt file (this happened few more times). The job is finished now but when I am trying to process the traj.trr file it shows an error after 20 ns and

[gmx-users] trajectory error

Dear all I have performed a 400 ns mdrun in GROMACS-2016.3. Due to some problem the job was crushed then I rerun the simulation using  state.cpt file (this happened few more times). The job is finished now but when I am trying to process the traj.trr file it shows an error after 20 ns an

[gmx-users] lifetime of hydrogen bond

Dear all I want to calculate the hydrogen bond lifetime of a dynamic hydrogen bond which stays for say 10 ns (as I have saved the trajectory with 10 ps interval).  I am trying to calculate the lifetime of this hydrogen bond by gmx hbond command gmx hbond -f traj_nopbc.trr -s md.tpr -n index.

Re: [gmx-users] lifetime of hydrogen bond

Thank you for your suggestion. - Message from David van der Spoel -     Date: Thu, 2 Jan 2020 08:28:17 +0100     From: David van der Spoel Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] lifetime of hydrogen bond       To: gmx-us...@gromacs.org Den 2020-01-02 kl. 07:47, s

Re: [gmx-users] cannot load the xtc file (without PBC) to VMD

Hii Have you tried with the .trr file? Try the same procedure with .trr file. Thanks - Message from Lalehan Ozalp -     Date: Mon, 13 Jan 2020 13:35:01 +0300     From: Lalehan Ozalp Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD  

Re: [gmx-users] cannot load the xtc file (without PBC) to VMD

I didn't get you. So your problem is solved using trr file or not? - Message from Lalehan Ozalp -     Date: Tue, 14 Jan 2020 12:53:54 +0300     From: Lalehan Ozalp Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD       To: gmx-us