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

[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] 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

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

[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

[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

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

[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] 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

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] 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

[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] 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

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] 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 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 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] "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:

[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] 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: 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,

[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

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] 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

[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

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 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 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/

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

[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] 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

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] 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] 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

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:

[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] 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

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

[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;

[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

[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] 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

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

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] 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

<    1   2