[gmx-users] pdb2gmx: intra-chain disulfide bond missing problem

Dear GROMACS users, Can I ask a disulfide bond question if possible? The link below is my protein L50K.pdb with 5 disulfide bonds. https://copy.com/kPLlSianI4LtohNy After using gmx pdb2gmx -f L50K.pdb -o L50K_processed.gro -water spce -inter -ignh -merge interactive one of the disulfide

[gmx-users] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?

Dear GROMACS experts, I am using pdb2gmx for a protein with 5 disulfind bond https://copy.com/kPLlSianI4LtohNy The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167. As a result, 10% margin of any value of the reference length in specbond.dat cannot cover all of the 5 Cys

[gmx-users] Syntax to use gmx convert-tpr

Dear GROMACS experts, Can I ask if the following commandlines are correct for extending simulations? gerun convert-tpr -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md_0_1.tpr gerun mdrun_mpi -deffnm md_0_1 -cpi md_0_1.cpt -maxh 0.5 -append (My job.sh can be found at

[gmx-users] Floating point exception for g_rms

Dear GROMACS experts, (Relevant files can be found on https://copy.com/7DMkn6OxJBqEZtqh) I have been told in the error file: ... ... Reading frame1700 time 17000.000 Reading frame1800 time 18000.000 Reading frame1900 time 19000.000 Reading frame2000 time 2.000

[gmx-users] how to assign options of the same type?

Dear GROMACS, Can I ask how to assign options of the same type? For example, on the website of http://manual.gromacs.org/current/programs/gmx-mdrun.html It is said in the Synopsis: [-o [.trr/.cpt/...] I want to name the output files as md.trr and md.cpt. However, the followings do not

[gmx-users] Can I ask how to extend my simulations?

Dear GROMACS, Can I ask how to extend my simulations? I would like to run a 50 ns job. Because of the cluster limitation, I need to use several jobs to complete that. ## Step1: grompp After using grompp on

[gmx-users] Can we convert one job into many serial jobs?

Dear GROMACS, I am now using openmpi nodes to run GROMACS (e.g. mdrun_mpi) on our cluster. When the nodes required are too many (e.g. more than 8), jobs always take a long time to wait in the queue. So I wonder if there is a possibility that we can 1) convert the job into many serial jobs?

[gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using -inter?

Dear GROMACS experts, Can I ask is there a more efficient way to deal with the -inter option in the pdb2gmx command? Now, I have to manually assign individual protonation status one by one, which takes a very long time. Sometimes I make a mistake and I have to re-do all of them again.

[gmx-users] echo 15 y 1 1 ...... failed for gmx pdb2gmx with -merge

Dear GROMACS researchers, I was trying to assign the protonation status in one go by the following: echo 15 y 1 1 1 .. | gmx pdb2gmx -f HC_A227E.pdb -o HC_A227E_processed.gro -water spce -inter -ignh -merge interactive In the commandline above, the .. means the protonation status for

[gmx-users] gromacs installing problems with "cmake .."

Dear Gromacs users, I got a list of errors after running "cmake ..". I am sure the "cmake" itself is already installed. I am installing Gromacs 5.1.4 on ubuntu-14.04.1 on VMwarePlayer on a Dell PC. Can I ask how to solve this? Thank you. Yours sincerely Cheng

Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

imulations, but is it for extending a completed job? In my case, I want to continue a incompleted job. Thank you. Yours sincerely Cheng ____ From: Zhang, Cheng Sent: 29 December 2016 18:23 To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: Zhang, Cheng Subject: How to extend my i

[gmx-users] How to extend my incompleted simulation? (not extend a completed one)

Dear Gromacs, I would like to extend my simulation. 200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr". Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr". Due to the limitation on our cluster, only 5 ns (for example) was simulated when the job finishes. The

Re: [gmx-users] How to extend my incompleted simulation? (not extend a completed one)

Hi Justin, Thank you very much. It worked as you said [] Yes, I was only using 10 min in the beginning, so no cpt file could be generated. Yours sincerely Cheng From: Zhang, Cheng Sent: 29 December 2016 19:02:47 To: gromacs.org_gmx-users

[gmx-users] Reading tpx file (md_0_1.tpr) version 110 with version 100 program

Dear Gromacs, I use "gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr" to generate the tpr file on my own PC. Then I submitted it to our university computer cluster, in which an older version is installed, and I got the Fatal error: Reading tpx file (md_0_1.tpr) version

[gmx-users] How to put excipients into the simulation box?

Dear Gromacs Researchers, Can I ask how to put excipients (e.g. sucrose, trehalose) into the simulation box together with protein, salt and water? Those excipients do not strongly interact with proteins, so they could not be treated as protein-ligand complex. I learned how to prepare the

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

4, 2017 02:12 AM To: "gmx-users"<gmx-us...@gromacs.org>; Subject: 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

[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

[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

[gmx-users] Magic Number Error in XTC file (read 0, should be 1995)

Dear Gromacs, I am trying to analyse my xtc file (40 ns) using: echo 0|gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact However, it shows: ... Fatal error: Magic Number Error in XTC file (read 0, should be 1995) ... Then I re-run the MD from the start from a

Re: [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)

filled with water and NaCl. -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 14, 2017 00:09 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sy

Re: [gmx-users] Magic Number Error in XTC file (read 0, should be 1995)

Can I ask if the procedure is correct? Would you please recommend some tutorial for prepare a system with protein and excipients (e.g. glycine, sorbitol, etc)? Thank you. -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 14, 2017 00:25 AM T

[gmx-users] How to use the index.ndx when running rms?

Dear Gromacs, After running echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx I got a index.ndx file. Then I run echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns But still only 18 options could be recognised. The index.ndx file is already in the same folder. So how to

Re: [gmx-users] How to use the index.ndx when running rms?

--- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 14, 2017 11:50 PM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: How to use the index.ndx whe

[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

Dear Gromacs, I am doing a MD for a protein with glycines. For glycine, I use ) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter and got ) gly.gro ) posre_gly.itp ) topol_gly.top For protein, I use ) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh

Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

in_chain_L 1 into [ molecules ] ; Compound#mols Protein_chain_L 1 (the "Protein_chain_L" refers to the protein) Protein 10 (the "Protein" refers to the glycine) ? -- Original -- Fro

Re: [gmx-users] How to obtain a proper structure for glycine?

3936GLY O19 0.047 -0.127 0.004 3936GLY O2 10 0.163 0.059 -0.0070.43801 0.27464 0.19713 -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Mon, Aug 7, 2017 02:20 AM To: "Mark Abraham"<mar

Re: [gmx-users] How to obtain a proper structure for glycine?

"gmx-users"<gmx-us...@gromacs.org>; "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Re: [gmx-users] How to obtain a proper structure for glycine? Hi, Prodrg is

Re: [gmx-users] How to use "gmx view" on Ubuntu?

help! Yours sincerely Cheng -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 04:27 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: Re: How to use "gmx vi

Re: [gmx-users] How to use "gmx view" on Ubuntu?

with the same issue "Compiled without X-Windows - can not run viewer." ) sudo apt-get install xorg-dev ) sudo apt-get install xorg-dev libglu1-mesa-dev (Sorry, I am not sure how to find the files to download) Thank you. Yours sincerely Cheng -- Original ------

[gmx-users] How to use "gmx view" on Ubuntu?

Dear Gromacs, I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS. When I run "gmx view ..." as below: gmx view -f dppc-md.xtc -s dppc-md.tpr I got the following: Compiled without X-Windows - can not run viewer. Can I ask how to use "gmx view" on Ubuntu? Thank you. Yours sincerely

Re: [gmx-users] How to use "gmx view" on Ubuntu?

to contain CMakeLists.txt. What I should do next? Thank you. Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, May 10, 2017 02:58 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kt

Re: [gmx-users] How to use "gmx view" on Ubuntu?

Dear Justin, Thank you for your link. I know how to install the Gromacs based on your link. But do you know where I can download the tar.gz file so that I can compile it and then use "gmx view"? Thank you. Cheng -- Original -- From: "ZHANG

[gmx-users] How the pH is reflected in Gromacs?

Dear Gromacs,I am simulating pH 4 condition. I interactively assign the protonation of chargeable residues of a protein based on PDB2PQR results by setting pH=4 in the "pKa Options" (http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/). I do not add citrate or acetate molecules to the simulation box. So

Re: [gmx-users] How to use "gmx view" on Ubuntu?

- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, May 11, 2017 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re: Re: How to use "gmx view" on Ubuntu? Dear Justin, Thank

[gmx-users] How to get the correct reference frame to run the rmsf?

Dear Gromacs, I try to use this command to calculate RMSF: echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq bfac.pdb -res -b 2 -e 3 My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is mandatory to assign a reference frame, so I use

[gmx-users] pdb2gmx do not work for unstable conformations

Dear Gromacs,I have a protein PDB structure as well as its mutants PDB, predicted by Rosetta with different ddG. After running pdb2gmx, I found that the structures with lower ddG (more stable) all perform okay; while structures with higher ddG (less stable) got fatal error: Fatal error:

Re: [gmx-users] pdb2gmx do not work for unstable conformations

-- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Sat, May 20, 2017 09:32 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: pdb2gmx do not work f

Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial

Dear Joao, Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that true that NVT needs to change two lines, while NPT and production run only need to change one line? Yours sincerely Cheng 1) In the NVT: ref_t = 370 370 ; reference temperature, one for each

[gmx-users] mdp file for 370 K MD based on Justin's tutorial

Dear Gromacs, I am performing 370 K MD based on Justin's tutorial. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html After "Step Five: Energy Minimization", I need to do NVT, NPT and a production run. I think I need to change 300 K to 370 K in three

[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Gromacs, I got this fatal error after running "pdb2gmx": Fatal error: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original ------

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Justin, Thank you very much. I will try the possible water models. Do you know if there are water models to resemble frozen state? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:5

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Joao, Thank you very much for your support. I am following Justin's tutorial but simulating a fragment of antibody (Fab). I will try the different water models. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com

Re: [gmx-users] "cmake" failed to install

Dear Mark and Mario, Thank you very much. I delete the gromacs and redo the cmake and it works now. Yours sincerely Cheng -- Original -- From: "mario";<ma...@exactas.unlpam.edu.ar>; Date: Thu, Jun 1, 2017 04:07 PM To: "ZHANG Cheng&qu

[gmx-users] "cmake" failed to install

Dear Gromacs, I did the below on Ubuntu 14.04: tar xfz gromacs-5.1.4.tar.gz cd gromacs-5.1.4 mkdir build cd build Then, I got error message when running: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON The error log files can be found here:

[gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume

Re: [gmx-users] "cmake" failed to install

- From: "mario";<ma...@exactas.unlpam.edu.ar>; Date: Thu, Jun 1, 2017 02:44 PM To: "gmx-users"<gmx-us...@gromacs.org>; Cc: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; "ZHANG Cheng"<272699...@qq.com>; Subject: Re: [gmx-use

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Justin, I replied the thread already, but it is waiting for approval due to large email content. Could you please approve it? Cheng ---Original--- From: "ZHANG Cheng"<272699...@qq.com> Date: 2017/5/19 22:37:52 To: "gromacs.org_gmx-users"<gromacs.org_gmx-u

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Justin, The command line that got fatal error is: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive The command line that works fine is: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge interactive (just

Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns 2) Is there a tutorial/manual for using python to extract coordinates at customised time and group? I will look at the "gmx traj -ox". Yours sincerely Cheng -- Original ------ From: "ZHANG Cheng&q

Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

-- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Nov 24, 2017 06:25 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Does RMSD only consider the "relative" coordinate changes for the

[gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

Dear Gromacs, When I calculate the RMSD for the whole protein, I got values mostly from 0.2-0.5 nm. However, when I only calculate for a particular residue (using an index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the loop. My understanding is: when doing the RMSD,

[gmx-users] Why the index file does not contain the indices I want?

Dear Gromacs, After running echo r 66 q|gmx make_ndx -f md_0_1.tpr -o index.ndx I got the index.ndx file. However, all the sections are those default ones, without the 66th residue atoms I want: [ System ] [ Protein ] [ Protein-H ] .. [ Ion ] [ NA ] [ CL ] [ Water_and_ions ] May I ask

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

"compressed-x-grps=Protein" will set xtc-grps as a group without waters and counterions? ------ Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Dec 15, 2017 08:34 PM To: "ZHANG Cheng"<272699...@qq.com>;&quo

Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?

; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off -- Original ------ From: "ZHANG Cheng";<272699...@qq.com>

[gmx-users] How to run MD with longer recording interval to reduce the file size?

Dear Gromacs, I am following Justin's tutorial of "Lysozyme in Water" to run the MD. The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less frequent intervals. In the md.mdp file, the "dt = 0.002". My understanding is to change the five "5000" into "5" to achieve

[gmx-users] How the index is recognised for values more than 99999?

Dear Gromacs,I am doing the RMSD calculation for a particular group of protein residues. My system also has water molecules so there are more than 9 atoms. Thus, the 10th atom is indexed as 0, and 11th atom as 1, and so on. So if the index file for my group has an entry of 1, how

Re: [gmx-users] How the index is recognised for values more than 99999?

m";<mark.j.abra...@gmail.com>; Date: Wed, Dec 6, 2017 04:34 AM To: "gmx-users"<gmx-us...@gromacs.org>; Cc: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; "ZHANG Cheng"<272699...@qq.com>; Subject: Re: [gmx-users] How th

Re: [gmx-users] What is the most reliable way to run repeats for reproducibility?

t.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jan 10, 2018 09:11 PM To: "gromacs.org_gmx-users"<gromacs.or

[gmx-users] What is the most reliable way to run repeats for reproducibility?

Dear Gromacs, I can think of different ways of running repeats, after reading Justin's lysozyme tutorial. The 1st way: all starting from the same em.tpr after energy minimization (EM) and use em.tpr individually for subsequent steps (NVT, NPT and production MD): ) repeat 1: same em.tpr ?? NVT

[gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

--- Original ------ From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 02:50 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I get the fraction of solvent accessible surface area using "gmx sasa&quo

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Alexandr, Thank you, but it is the same with spaces between | :( Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 06:37 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kt

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

quot;? Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

-s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns I got: 0.0002.767 0.1002.757 0.2002.736 ... ... Do you know what is the meaning of the second column? Thank you! -- Original -- From: "ZHANG Cheng";<

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

.901/2.736 ... ... -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 08:02 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re:Can I get the fraction of solvent accessible su

[gmx-users] Which files does "-cpi -append" need?

Dear Gromacs, I run Gromacs on our cluster, and use this command to continue my run from last checkpoint. gmx mdrun -deffnm md_0_1 -cpi -append Each new run will generate four log files: md_0_1.e md_0_1.o md_0_1.pe md_0_1.po Gradually, I have thousands of log files. So I used these

Re: [gmx-users] Which files does "-cpi -append" need?

Thank you very much Justin! Sorry I did not realise that. I will need to include an "except md_0_1.edr" in the deletion. But does it correct that I can delete all the log files? md_0_1.e md_0_1.o md_0_1.pe md_0_1.po -- Original -- From: &q

[gmx-users] Why gyration radius keep dropping?

Dear Gromacs, I am running MD at 500 K for my protein. I used this to analyse the gyration radius echo 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg I thought the radius should keep increase, as the protein unfolds at high temperature. However, all my repeats showed a

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

I got it, Thank you very much for all the help! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 08:46 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Re

[gmx-users] Alternative for do_dssp for secondary structure analysis?

Dear Gromacs, Can I ask if there is an alternative to do_dssp for secondary structure analysis? I am waiting for our IT staff to install the DSSP on our cluster. But there was some errors. https://github.com/UCL-RITS/rcps-buildscripts/issues/137 While still waiting for that, can I ask if

[gmx-users] How to use "gmx editconf -bf" to assign b-factor values to a PDB containing multiple frames?

Dear Gromacs, I am using: gmx editconf -f protein.pdb -bf bf.dat -o bf.pdb to assign b-factor values to "protein.pdb", which contains multiple pdb frames. However, the output "bf.pdb" only includes the first frame. Can I ask is there a way to assign b-factor values to all the frames of one

Re: [gmx-users] Can I put b-factor into xtc file?

- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Fri, Feb 2, 2018 04:44 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Can I put b-factor into xtc file? Dear Gromacs, I have residue-based b-factor va

[gmx-users] Can I put b-factor into xtc file?

Dear Gromacs, I have residue-based b-factor values for a protein. In the past, they were assigned to the b-factor columns of pdb files. It would take a lot of space if I extract all the pdb files. As the pdb files come from the xtc file, I wonder, if I can modify the xtc file directly? Thank

[gmx-users] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?

Dear Gromacs, The scount.xvg file was obtained after running echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns The secondary structures listed are:

[gmx-users] Why "do_dssp" gives one more residue?

Dear Gromacs, My protein only has 442 residues. After running gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to

Re: [gmx-users] Why "do_dssp" gives one more residue?

~~" Do you think the 443th line is the separator? So ignore the 443th line? ------ Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Thu, Feb 22, 2018 01:20 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.

Re: [gmx-users] Why "do_dssp" gives one more residue?

- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Thu, Feb 22, 2018 01:34 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Why "do_dssp" gives one more residue? Dear Qinghua, Yes, exactly! But the numb

[gmx-users] How to search answers for previous posts?

Dear Gromacs, I know I can see all the post from https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ but can I search from this link? I do not want to download all of them to my PC. Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at

[gmx-users] chain separator issue for the "gmx do_dssp": do NOT need to provide a "ss.map" file

I would like to share my answer for chain separator issue for the "gmx do_dssp". Millions of thanks to Carsten! The "gmx do_dssp" will output an additional line as chain separator between two chains. We do NOT need to provide a "ss.map" file in our working directory, and the command will find

Re: [gmx-users] chain separator issue for the "gmx do_dssp": do NOT need to provide a "ss.map" file

0.5 0.5 0.5 = Chain_Separator 0.9 0.9 0.9 -- Original ------ From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Apr 6, 2018 10:13 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@mai

[gmx-users] ss.xpm file: chain separator location? first residue showing first, or last residue showing first?

Dear Gromacs, (Sorry I post this again as I have not got confirmed answer yet) In the ss.xpm file for secondary structures, can I ask if the first residue shows first, or last residue shows first? I could not find the description in the file. I also have a chain separator. Can I ask does it

[gmx-users] why "gmx gyrate" could not be supplied with "-tu ns" option?

Dear Gromacs, I use Command line: gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg -tu ns and was told: Error in user input: Invalid command-line options Unknown command-line option -tu So why "gyrate" could not be supplied with "-tu ns" option? Thank you. Yours

[gmx-users] ss.xpm file: first residue showing first, or last residue showing first?

Dear Gromacs, In the ss.xpm file for secondary structures, can I ask if the first residue shows first, or last residue shows first? Is this already written in the file? I also have a chain separator. Can I ask does it show in the beginning or between the two chains? (Sorry, I asked this

[gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to replace the "define = -DPOSRES" option in the .mdp file. However, how can I do position restraints only for certain atoms, e.g. only the backbone atoms? I think, if I use "-r target.pdb", both the backbone and side chain

Re: [gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

on_restraints ]" section in the itp file ) the only difference is, add "-r target.gro" where the "target.gro" can be the same as that for "-c" option. Thank you very much! Cheng -- Original -- From: "ZHANG Cheng"&

Re: [gmx-users] Use all-atom PDB or coarse-grained PDB as the restraints for grompp a coarse-grained gro?

Sorry for asking this. I now understand it. See post at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/123809.html -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Wed, Jan 16, 2019 04:27 AM To: "

[gmx-users] How the "Fmax" is determined without "emtol" in the mdp file?

I am doing an energy minimization in a vacuum condition. There is no "emtol" in the mdp file. The energy converges in the end, and tell me "Fmax < 10" as shown below. So how this "< 10" is determined? Steepest Descents converged to Fmax < 10 in 4063 steps Potential Energy = -2.3973977e+04

Re: [gmx-users] How the "Fmax" is determined without "emtol" in the mdp file?

Thank you so much, Justin and Mark! -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 18, 2019 09:55 PM To: "gromacs.org_gmx-users"; Subject: How the "Fmax" is determined without "emtol&

[gmx-users] How to visualise the dodecahedron in Pymol or VMD?

I use gmx editconf -f protein.pdb -d 5 -bt dodecahedron -o protein.gro to put the protein in a dodecahedron. However, when I open the protein.gro in pymol, and type "show cell", only a triclinic box is shown. So how to visualise the dodecahedron in Pymol or VMD? -- Gromacs Users mailing

[gmx-users] why .top file is not updated with added waters in "gmx solvate" if customised water.gro is provided?

In the command gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768 -radius 0.21 -p dppc.top 768 waters are added, resulting in the "waterbox.gro". However, the "dppc.top" is not updated for its "[ molecules ]" section. I can of course manually add that. But why it

Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

"-r 1UBQ-CG.pdb"? So the whole command is the below? gmx grompp -p system.top -r 1UBQ-CG.pdb -c solvated.gro -f minimization.mdp -o minimization.tpr ------ Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Mon, Jan 14, 2019 10:16 PM

Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

and the "Protein_A.itp" file has the restraints I need. Should I modify the "minimization.mdp" instead? -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Mon, Jan 14, 2019 09:53 PM To: "gromacs.org_gmx-u

[gmx-users] Use all-atom PDB or coarse-grained PDB as the restraints for grompp a coarse-grained gro?

In Gromacs 2018, -r is used to provide the restraint file for grompp. I have a grompp command used for a coarse-grained (CG) gro file, i.e. CG.gro: gmx grompp -f parameter.mdp -r AllAtom.pdb/CG.pdb -c CG.gro -p system.top -o MD.tpr So in the command above, should I use AllAtom.pdb or CG.pdb

[gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told "Too many LINCS warnings" in the minimization after solvation with coarse-grained waters. I try to diagnose the problems based on http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

am using this, but I do not know how to modify it. https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 22, 2019 00:12 AM To: "gromacs.org_gmx

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

ential Energy = -2.4130119e+05 $ Maximum force = 9.1535597e+00 on atom 2335 $ Norm of force = 7.1063030e-01 Peter, how to replace all constraints for stiff bonds? -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date

Re: [gmx-users] How to install a new force-field?

Thank you very much! I got it now! Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Sun, Dec 23, 2018 10:54 PM To: "gromacs.org_gmx-users"; Subject: Re: How to install a new force-field? Thank you Just

[gmx-users] How to install a new force-field?

Dear Gromacs users, In the pdb2gmx command, we are asked to select the force field to simulate our protein system. I am told that a99SB-disp and CHARMM36m are better force-field for the proteins. But both of them are not the default ones. Can I ask 1) What is the latest officical website to

Re: [gmx-users] How to install a new force-field?

Thank you Justin. Do you know how to use the "define = -DUSE_OLD_C36" as shown on http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs I want to make sure the CHARMM36m is used instead of CHARMM36. -- Original -- From: "ZHANG Cheng&qu

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