Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

doable. But do you think simulating one protein without its neighbours could reflect its dynamics? Would its boundary residues behave very differently compared to with neighbours? --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Wed, Apr 8,

Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

le for our university to provide. --Original------ From:"ZHANG Cheng"<272699...@qq.com; Date:Tue, Apr 7, 2020 10:10 PM To:"ZHANG Cheng"<272699...@qq.com;"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_R

Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

time is not reduced, as now only several proteins are simulated. If I simulate all the several protein without any fixing, I worry they will lose their conformation. So fixing the neighbours and only focusing on the protein in the centre could be the solution. ------Original

[gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

It is a challenge to simulate the entire virus as it is too big and I do not have such computational resources. So I was thinking to only simulate one coat protein and its surrounding neighbours, but keep the neighbours relatively fixed. Can I ask 1) Is this a sensible idea to proceed? 2)

Re: [gmx-users] PCA analysis with different atoms in -s and -f

of time length"? Thank you! Yours sincerely Cheng --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Wed, Apr 1, 2020 09:10 AM To:"gromacs.org_gmx-users"http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] PCA analysis with different atoms in -s and -f

I am trying to compare trajectories from different MD simulations, including different pH and different mutants. The initial PDB (i.e. 0.pdb) is the same, but the derived PDBs (1.pdb, 2.pdb, etc.) are different due to protonation states and mutations. Those different PDBs were used individually

[gmx-users] Clarification on the "-surface" and "-output" options of "gmx sasa"

Dear Gromacs, There seems to be very little explanation on the "-surface" and "-output" options of "gmx sasa": -surface: This should always consist of all non-solvent atoms in the system. The area of this group is always calculated -output: can specify additional selections, which should be

Re: [gmx-users] Automatically assign the protonation states for pdb2gmx

Thank you Mark! I have triedversion 2019.3 as well. Again, the manual input works all fine https://github.com/lanselibai/gromacs-20200223/blob/master/manually_type but the command using "echo" still had the same problem https://github.com/lanselibai/gromacs-20200223/blob/master/echo I also

Re: [gmx-users] Automatically assign the protonation states for pdb2gmx

mx pdb2gmx, version 2020-beta2 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 130) Fatal error: Answer me for res GLUTAMINE 3! --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Sat, Feb 22, 2020 04:39 AM To:"gromacs.org_gmx-users&

[gmx-users] Automatically assign the protonation states for pdb2gmx

I want to run more than 300 MD, each with a different PDB (more precisely, variants derived from a same wild type). I need to manually assign the protonation states using the "-inter" option every time, which is impossible for more than 300 times. gmx pdb2gmx -f protein.pdb -o

[gmx-users] Native contacts similar to "gmx mindist"

The "gmx mindist?? command can output the number of contacts (numcont) between two groups as a function of time. Is there a way to only consider the native contacts, without using the PLUMED? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to run REMD for EM, NVT, NPT and production run?

I have gone through Mark Abraham's tutorial on REMD http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B Now I would like to run my own REMD, adjusted from Justin's Lysozyme tutorial

[gmx-users] How to set the temperatures for REMD?

My purpose of running REMD is to generate sufficient conformation sampling, and try to use them to explain the in vitro data at 65C (338.15K). I am using the "Temperature generator for REMD-simulations" at http://folding.bmc.uu.se/remd/ I am not sure about the "standard/default" values of

[gmx-users] Assertion failed for the REMD tutorial

I am trying to follow the REMD from Mark Abraham at http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B At Stage 2, when I run the grompp command (for dir in sim[0123]; do cd $dir;

Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

ppend" ? --Original------ From:"ZHANG Cheng"<272699...@qq.com; Date:Fri, Jan 17, 2020 00:57 AM To:"gromacs.org_gmx-users"https://github.com/lanselibai/gromacs-20200116 The MD is run on our HPC cluster. So I personally could not compile it. Is there

Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

-20200116 The MD is run on our HPC cluster. So I personally could not compile it. Is there still some way to get equivalent performance for the Version 2019? --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Thu, Jan 16, 2020 07:58 AM To:

Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

Hi Justin, what kind of information should I look at in the log files? They are too big to paste here. Would it be possible if you can see them athttps://github.com/lanselibai/gromacs-20200115;? Thank you! --Original-- From:"ZHANG Cheng"<272

[gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and

Re: [gmx-users] How to set more mpi for the REMD run?

Thank you very much Paul, I got it! --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Mon, Nov 11, 2019 09:57 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Works

Re: [gmx-users] How to set more mpi for the REMD run?

Thank you Paul! I want to use more than one mpi processes for each of the REMD, would it be possible? --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Mon, Nov 11, 2019 09:39 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/

[gmx-users] How to set more mpi for the REMD run?

I am using the same files based onMark Abraham's REMD tutorial, except using a recent Gromacs version (gromacs/2019.3).http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B For Stage

Re: [gmx-users] How to use gmx_mpi?

to make it correct? --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Sat, Nov 9, 2019 06:11 AM To:"gromacs.org_gmx-users"http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://

[gmx-users] How to use gmx_mpi?

Dear Sir or Madam, I use this in my job.sh file: #!/bin/bash -l #$ -S /bin/bash #$ -l h_rt=01:00:0 #$ -l mem=2G #$ -l tmpfs=15G #$ -N REMD #$ -pe mpi 12 #$ -cwd module load gcc-libs module load compilers/intel/2018/update3 module load mpi/intel/2018/update3/intel module load

[gmx-users] What is the equivalent command for insert-molecules in Gromacs 3.3.1?

Dear All, Due to a software that is only compatible to Version 3.3.1, I have to use that to prepare the simulation box. I was told "command not found?? when using the insert-molecules. So what should I do to put multiple molecules in a box? Thank you! Cheng -- Gromacs Users mailing list

Re: [gmx-users] Can I align individual domains (not the whole structure) in the RMSD?

-- From: "ZHANG Cheng"<272699...@qq.com>; Date: Wed, Feb 27, 2019 01:09 AM To: "gromacs.org_gmx-users";"ZHANG Cheng"<272699...@qq.com>; Subject: Can I align individual domains (not the whole structure) in the RMSD? My protein Fab has V

[gmx-users] Can I align individual domains (not the whole structure) in the RMSD?

My protein Fab has VH, VL, CL, CH domains. Usually in the RMSD calculation, I align the whole Fab first, then use a index file to calculate the domain's RMSD: $ echo 1 19 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx (Group 1 is the whole protein, Group 19 is one of

Re: [gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?

to optimise the cpu and memory with the least queue time. Thank you! -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Feb 19, 2019 05:13 AM To: "gromacs.org_gmx-users"; Subject: Is there a more efficient way to c

[gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?

My coarse-grained system has 10 proteins, each has 442 residues. After a period of time, those proteins aggregated. I want to use "gmx distance" to know which residues most likely to involve contact with other proteins. I prepared a index.ndx file, in which there are 442*442*(9+8+7 ... + 1) =

Re: [gmx-users] syntax for index file in "gmx distance"

I think I know now: gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -select 'group 0 plus group 1' -oall -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Sun, Feb 17, 2019 08:06 PM To: "gromacs.org_gmx-user

[gmx-users] syntax for index file in "gmx distance"

My gro file looks like this $ Martini system from C226S.pdb $ 72758 $ 1ASP BB1 15.982 3.547 3.592 $ 1ASPSC12 15.989 3.335 3.842 $ 2ILE BB3 15.668 3.625 3.593 $ 2ILESC14 15.538 3.345 3.620 $ 3GLN BB5 15.590 3.886

Re: [gmx-users] How to use "echo" to output index file with only one command line?

Dear Pedro Deira, Sorry, could you please show me how to include the newline using "echo" with only one command line? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Mon, Feb 11, 2019 06:36 AM T

[gmx-users] How to use "echo" to output index file with only one command line?

I can successfully output the index file by doing it step by step: $ gmx make_ndx -f equilibration.gro $ r 1-442 $ q But I am not sure how to do it in just one line. I tried these but all could not work $ echo r 1-442 q | gmx make_ndx -f equilibration.gro $ echo "r 1-442" q | gmx make_ndx

[gmx-users] More details on the "Steepest Descents"

Dear Gromacs friends, I am trying to understand more on the "Steepest Descents" so that I can decide if I need to better minimise the system by reducing the "emtol" or increasing the "nsteps", or other ways. The prompt is shown in the end. My understanding is, the algorithm randomly chooses

[gmx-users] martini: How do I know if the coarse-grained (CG) ions are added?

I use these two lines to neutralise the system $ gmx grompp -f minimization.mdp -r system-solvated.gro -c system-solvated.gro -p system.top -o system_genion.tpr $ echo W | gmx genion -s system_genion.tpr -o system_genion.gro -p system.top -pname NA -nname CL -neutral -conc 0.2 (#include

[gmx-users] martini: clarification on the Particle definitions (i.e. force field)

Dear martini friends, (Sorry for still posting here as the martini forum does not get reply quickly) I am evaluating which force field mostly suits my protein. From this link http://www.cgmartini.nl/index.php/force-field-parameters/particle-definitions there are 7 martini 2.x options to choose,

Re: [gmx-users] martini: what is the column position if "ASP" is changed to "ASP0" in the itp file?

Dear Peter, Thank you very much! Yours sincerely Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Feb 1, 2019 09:47 PM To: "gromacs.org_gmx-users"; Subject: martini: what is the column position if

[gmx-users] martini: what is the column position if "ASP" is changed to "ASP0" in the itp file?

Dear Martini users, I want to change some chargeable residues into neutral forms. e.g. change "ASP" to "ASP0". If the column is indexed from 1 (not from 0), the "ASP" column positions are 21-23. So, if "ASP0" is used, should their column positions be 20-23 or 21-24 in the itp file? Thank

Re: [gmx-users] How to set the inter-chain disulfind bond in martini?

can shown in the generated itp file. If "-merge" is missing, only the intra-chain SS bonds are shown in the individual itp files. So happy to see the martini forum come back! Yours sincerely Cheng -- Original ------ From: "ZHANG Cheng"<2726

[gmx-users] How to set the inter-chain disulfind bond in martini?

Dear Martini friends, My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy chain (HC): ) Interchain disulfide bond: LC214 ?C HC220 ) Intrachain disulfide of LC: LC23 ?C LC88, LC134 ?C LC194 ) Intrachain disulfide of HC: HC144 ?C HC200, HC96 ?C HC22 Using this command

Re: [gmx-users] How to adjust the default protonation states in martini itp files?

Dear Peter, Thank you very much! I will use GLU0 and -nt. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 29, 2019 08:38 AM To: "gromacs.org_gmx-users"; Subject: How to adjust the

[gmx-users] How to adjust the default protonation states in martini itp files?

Dear martini friends, By default, the "martinize.py" will 1) for backbone atoms, positively charge the N-terminus (atom type Qd), and negatively charge the C-terminus (atom type Qa). 2) for side chain chargeable residues, always positively charge the LYS and ARG and negatively charge the

Re: [gmx-users] What is the difference of using "system" and separating groups for "tc-grps"?

Thank you very much Eric Smoll! I will use "tc_grps = Protein Non-Protein". -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Mon, Jan 28, 2019 09:45 AM To: "gromacs.org_gmx-users"; Subject: Wha

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

box. Then fill the system with that minimised water box. Problem solved! Best Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Tue, Jan 22, 2019 10:20 PM To: "gromacs.org_gmx-users"; Subject: Re: Re:

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] "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

[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

[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 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 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

[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

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: "

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"&

[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

[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

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] How to use "define = -DPOSRES" in Gromacs 2018?

My backbone restraints is shown in the "Protein_A.itp" file: #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FC

[gmx-users] How to make a gro water model from a a99SB-disp force field?

I got the a99SBdisp force field with a tip4pd.itp water model. How can I convert it to a tip4pd.gro file? I need this water gro file for "gmx solvate". Thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?

Thank you Justin and Mark. Using "-water select" works: Select the Water Model: 1: TIP4P-D TIP 4-point with increased dispersion 2: None -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:51 AM T

Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?

Invalid command-line options In command-line option -water Invalid value: tip4pd -- Original ------ From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:31 AM To: "gromacs.org_gmx-users"; Subject: Re: Why pdb2gmx could

Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?

Thank you Justin. The "watermodels.dat" and "tip4pd.itp" are already in the ff subdirectory. The "watermodels.dat" content is: tip4pd TIP4P-D TIP 4-point with increased dispersion But "-water tip4pd" still has the error. ------ O

[gmx-users] Why pdb2gmx could not accept tip4pd as the water model?

I got the a99SB-disp forcefield with tip4pd.itp as the water model. The a99SB-disp.ff file has been copied: "/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff" The tip4pd.itp file has also been copied to "/usr/local/gromacs/share/gromacs/top" However using "-water tip4pd" in "pdb2gmx" will

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

is the directory of $GMXLIB? Thank you. Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Sun, Dec 23, 2018 11:01 PM To: "gromacs.org_gmx-users"; Subject: Re: Re: How to install a new force-field? Thank you very m

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

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

[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] 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] 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

[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] 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] 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] 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] 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:

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

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.

[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

[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] 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] 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] 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] 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] 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

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

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"?

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"?

--- 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

[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] 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

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

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

[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] 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

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

[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,

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