Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Andre, Thank you. We are trying to use an adenovirus as a vaccine. As it is not stable, we want to simulate it to identify the unstable regions (e.g. flexible), so as to either engineering (e.g. mutation) it, or adding excipients. Simulating only one protein of the capsid is of course 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, 2020 11:02 AM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Justin and Andre, Thank you for the advice. So can I ask how commonly the very large virus capsid is simulated? A recent paper "Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations" is using 3880 GPU accelerated Cray-XK nodes, which is impossible 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_Restraints Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Andre, Thank you for the advice. Can I ask, 1) Could you please clarify the concepts? I know "constraint" and "restraint" are two different things in gromacs. And "fix" is another term? How about "freezegrps"? 2) It is okay that the computational 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-- From:"ZHANG Cheng"<272699...@qq.com; Date:Tue, Apr 7, 2020 09:41 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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) To fix the neighbours, should I use "constraints" or "restraints"? 3) At which step should I start to introduce the fixation? 4) If possible, is there a tutorial for this? I feel the information here is still not straightforward to follow http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PCA analysis with different atoms in -s and -f
Dear Eduardo, Many thanks for your detailed explanation. Sorry I am not an expert on the PCA. So I may need more explanations from you if you do not mind. Feel free to correct if I am wrong. I have done the common analysis to the MD run at different conditions, including RMSD, Rg, secondary structure, native contacts, etc. I can find some differences among those conditions. But I feel that there are infinite properties to choose to compare. So I am trying to find a more systematic way to quantify the difference. I found the "gmx anaeig -over" seems to be an ideal option. Can I ask, 1) How the "-ref" is used in the PCA analysis? i.e. How the "deviation" is used in the process of PCA? Do I need to fully understand the mathmatical equations in order to understand it? # -ref no (default) Use the deviation from the structure file (i.e. -s name.pdb) # -ref yes Use the deviation from the average of the trajectories 2) So far, I choose "MainChain" as the least square fit, and "C-alpha" for the PCA. I hope I can see the significant difference between the different conditions at the C-alpha level. But if not, I may choose "Backbone" or "MainChain" for the PCA. 3) Can you explain what is "long enough to have at least two halves of trajectory 0.pdb CA. 100% overlap of covariance matrices", and what is "block analysis to calculate overlap error as a function 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? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 for the MD. To obtain the eigen vectors, should I use the 0.pdb as the reference structure? # gmx covar -s 0.pdb -f 1.xtc -v 1.trr (use 0.pdb as reference, and calculate the eigen vectors from trajectories of 1.pdb) The first is to choose the least squares fit. Though the atoms in "Protein", "Protein-H" are different between 0.pdb and 1.xtc, they are same in "C-alpha", "Backbone" and "MainChain". However, when I choose "C-alpha" for the "least squares fit", I still got the warning: # WARNING: number of atoms in tpx (442) and trajectory (6622) do not match The calculation can still be done. So must I provide "1.pdb" as reference for "1.xtc", or is it still okay to use "-s 0.pdb"? Afterwards, I want to run # gmx anaeig -s 0.pdb -over overlap_1_2.xvg -v2 1.trr -v 2.trr to compare the similarity between Condition 1 and Condition 2. Is this correct? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 subsets of the calculation group. Can I understand in this way: 1. The "-surface" will calculate the surface area of the suppiled group. Regardless the group is inside or outside of the protein, the "sasa" will always assume the group to be fully solvent-exposed. So actually, it is not "Solvent Accessible Surface Area" of the group; it is "taking the group out from the protein, and put it in solvent, then calculate its surface". 2. When all the residues are supplied to the "-output" option, I have tested that the sum of "-output" equals to the "-surface": gmx sasa -s protein.pdb -o area.xvg -tu ns -surface 'group 1' -output 'resnr 1; resnr 2; resnr 3; ...; resnr n' This is good. However, I saw many residues having area of 0 even though they locate on the very outer surface. I think the explanation could be, their side-chains are totally shielded by their neighbouring side-chains. Is that correct? (I just feel SASA value of 0 is almost impossible) Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@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 uploaded my protein.pdb at (it would be great if you can test it?) https://github.com/lanselibai/gromacs-20200223/blob/master/protein.pdb but I think it is not the pdb issue, also not the Gromacs version problem. I took a look at the meaning ofstdin, stdout, and stderr. So do you mean "echo" is used in the "stdin"? Basically, do you mean it should be possible to use "echo"? I am sure I have supplied enough numbers to the "echo". echo 15 0 0 0 0 |gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge interactive Here, ) "15" is to choose the OPLS forcefield; ) The second and third number "0" is to assign the charges; ) The last two "0" is to select the terminus type. --Original-- From:"Mark Abraham"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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Automatically assign the protonation states for pdb2gmx
Thank you Mark! Sorry could you please explain the details of "stdin" of "pdb2gmx"? Is there a link for it? I think "echo" only works for choosing the force field, but not work for the charge assignment. e.g. when I use: echo 15 0 0 0 0 | gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge interactive I got error message: Which GLUTAMINE type do you want for residue 3 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number: --- Program: gmx 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"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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 protein_processed.gro -water spce -inter -ignh -merge interactive The protonation states come from the pdb2pqr website. Is there an alternative way to obtain the .gro file by providing the necessary inputs (e.g. pdb, protonations), so that I can batch obtain the 300 corresponding .gro files? I know the "echo" could not work for the charge assignment. It would be ultimately possible if I can understand the fundamental codes behind "pdb2gmx", then write a batch code to process multiple PDB files at once. But is there a simpler route? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 (is this correct?) http://www.mdtutorials.com/gmx/lysozyme/index.html Can I ask, 1) The normal MD involves EM, NVT, NPT and production run, while the REMD in the tutorial involves Stage 1 of equilibration and Stage 2 of production run. Should I run normal MD for EM and NVT, and run REMD for NPT and production run? 2) How many steps should be used for the "-replex" option in the production run? The REMD tutorial uses 100, is this generally applicable? My protein is ~50 kDa. Thank you! -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 several parameters. Can I ask how to determine them? 1) Exchange probability: it should be a value between 0 to 1. The higher of the value I set, the shorter intervals of the temperatures are output. 2) Tolerance: by default it is 1e-4. So I just use it? 3) Lower/Upper temperature limit: As I am interested in 338.15K, should the lower limit set to be 338.15K, while the upper limit as 373.15K (i.e.100C)? Should it be even higher? 4) Constraints in water: Fully flexible? 5) Constraints in the protein: All bonds? 6) Hydrogens in protein: All H? (what does this mean?) Is there a general rule for the number of temperatures used in the REMD? Please feel free to tell me if there is a guidelines for setting the temperatures. Thank you! -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 grompp -f sim -c confout -t equil-state; cd ..; done) I got error message: Program: gmx grompp, version 2019.3 Source file: src/gromacs/fileio/checkpoint.cpp (line 591) Function: lambda []()-auto::operator()()-auto Assertion failed: Condition: list != nullptr || (v != nullptr vector == nullptr) || (v == nullptr vector != nullptr) Without list, we should have exactly one of v and vector != NULL The whole log is uploaded at https://github.com/lanselibai/gromacs-20200121/blob/master/Assertion%20failed.log Can I ask how to solve this? Thank you! -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
Many thanks for Justin's advice forassigning the same number of PP and PME ranks in each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not familiar with these kind of settings, can I ask how to do this exactly? e.g. how to change "gmx mdrun -deffnm md_0_1 -cpi -append" ? --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 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:"ZHANG Cheng"<272699...@qq.com;"gromacs.org_gmx-users"https://github.com/lanselibai/gromacs-20200115;? Thank you! -- Original -- From:"ZHANG Cheng"<272699...@qq.com; Date:Thu, Jan 16, 2020 03:38 AM To:"gromacs.org_gmx-users"http://www.mdtutorials.com/gmx/lysozyme/index.html The commands I used are listed below. gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce -inter -ignh -merge interactive gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05 (Afterwards, using the HPC to run) gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr gerun mdrun_mpi -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro gerun mdrun_mpi -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro gerun mdrun_mpi -deffnm npt gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro gmx mdrun -deffnm md_0_1 -cpi -append -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?
I have re-run the MD, with only 2 ps in both version. Indeed, the Version 2019 is far slower than the Version 5.1.1. Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1 only needs6.362 hours to complete 1 ns. The new logs files are at https://github.com/lanselibai/gromacs-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:"ZHANG Cheng"<272699...@qq.com;"gromacs.org_gmx-users"https://github.com/lanselibai/gromacs-20200115;? Thank you! -- Original -- From:"ZHANG Cheng"<272699...@qq.com; Date:Thu, Jan 16, 2020 03:38 AM To:"gromacs.org_gmx-users"http://www.mdtutorials.com/gmx/lysozyme/index.html The commands I used are listed below. gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce -inter -ignh -merge interactive gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05 (Afterwards, using the HPC to run) gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr gerun mdrun_mpi -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro gerun mdrun_mpi -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro gerun mdrun_mpi -deffnm npt gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro gmx mdrun -deffnm md_0_1 -cpi -append -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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"<272699...@qq.com; Date:Thu, Jan 16, 2020 03:38 AM To:"gromacs.org_gmx-users"http://www.mdtutorials.com/gmx/lysozyme/index.html The commands I used are listed below. gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce -inter -ignh -merge interactive gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05 (Afterwards, using the HPC to run) gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr gerun mdrun_mpi -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro gerun mdrun_mpi -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro gerun mdrun_mpi -deffnm npt gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro gmx mdrun -deffnm md_0_1 -cpi -append -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 production run, respectively. Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD? I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html The commands I used are listed below. gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce -inter -ignh -merge interactive gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05 (Afterwards, using the HPC to run) gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr gerun mdrun_mpi -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro gerun mdrun_mpi -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro gerun mdrun_mpi -deffnm npt gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro gmx mdrun -deffnm md_0_1 -cpi -append -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B For Stage 1 of the tutorial, when "#$ -pe mpi 4" is used, it can be run successfully: gerun mdrun_mpi -v -multidir ./equil[0123] However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? Program: mdrun_mpi, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 6 (out of 12) Fatal error: There is no domain decomposition for 3 ranks that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B For Stage 1 of the tutorial, when "#$ -pe mpi 4" is used, it can be run successfully: gerun mdrun_mpi -v -multidir ./equil[0123] However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? Program: mdrun_mpi, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 6 (out of 12) Fatal error: There is no domain decomposition for 3 ranks that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@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 1 of the tutorial,when "#$ -pe mpi 4" is used, it can be run successfully: gerun mdrun_mpi -v -multidir ./equil[0123] However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? Program: mdrun_mpi, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 6 (out of 12) Fatal error: There is no domain decomposition for 3 ranks that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to use gmx_mpi?
I think I managed to use the correct command: mpirun -np 12 gmx_mpi mdrun -v -multidir ./equil[0123] However, I was told [proxy:0:0...@node-e00a-002.myriad.ucl.ac.uk] HYDU_create_process (../../utils/launch/launch.c:825): execvp error on file gmx_mpi (No such file or directory) So how 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://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 gromacs/2019.3/intel-2018 gmx_mpi mdrun -np 12 mdrun_mpi -v -multidir equil[0123] But I was told "gmx_mpi: command not found". So how to correct it? Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 * 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can I align individual domains (not the whole structure) in the RMSD?
Sorry, can someone help me with this question? I think this question is very important, though it seems to be very basic. I can see in many publicationis, the authors do not explicitly state how the alighment is done for the RMSD. Thank you! Cheng -- Original -- 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 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 the domains) Now I was told to align the domain only, and then calculate the RMSD of that domain: $ echo 19 19 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx $ echo 20 20 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx $ echo 21 21 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx $ echo 22 22 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx because we want to see if the domain itself has changed (e.g. unfolded) throughout the trajectories, and compare which domain deforms mostly. If the whole structure is aligned, then the RMSD of each domain will be influenced by the alignment of the whole. I can understand this saying. But is this really fair to align each domain? Is this a common practice? Also, in most cases, the domain with more residues would have higher RMSD if each domain is aligned. Thank you! Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 the domains) Now I was told to align the domain only, and then calculate the RMSD of that domain: $ echo 19 19 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx $ echo 20 20 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx $ echo 21 21 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx $ echo 22 22 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx because we want to see if the domain itself has changed (e.g. unfolded) throughout the trajectories, and compare which domain deforms mostly. If the whole structure is aligned, then the RMSD of each domain will be influenced by the alignment of the whole. I can understand this saying. But is this really fair to align each domain? Is this a common practice? Also, in most cases, the domain with more residues would have higher RMSD if each domain is aligned. Thank you! Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Is there a more efficient way to calculate the "gmx distance" with a very long index?
Can I also ask, I am running it on high performance computer (HPC). So whether the cpu (-pe mpi 12) or memory (-l mem=2G) would influence the capability to handle a very long index file? When the job is submitted, longer queue time will be required if requesting more resources. So I want 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 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) = 8791380 pairs of atom indices. But these indices are extremely too long for Gromacs to handle at a time. So I have to split it into shorter pieces. But is there a more efficient way to achieve this? Thank you! Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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) = 8791380 pairs of atom indices. But these indices are extremely too long for Gromacs to handle at a time. So I have to split it into shorter pieces. But is there a more efficient way to achieve this? Thank you! Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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-users"; Subject: 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 3.462 $ 3GLNSC16 15.908 4.021 3.297 I tried: $ gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -oall in which the index.ndx is $ [ atom ] $ 1 $ [ atom ] $ 19 But I was told: $ Available static index groups: $ Group 0 "atom" (1 atoms) $ Group 1 "atom" (1 atoms) $ Specify any number of selections for option 'select' $ (Position pairs to calculate distances for): $ (one per line, for status/groups, 'help' for help, Ctrl-D to end) How should I proceed with this? Is there a simple example example for the index.ndx? I could not find good answers at http://manual.gromacs.org/archive/5.0.3/online/ndx.html http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-distance.html Thank you. Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 3.462 $ 3GLNSC16 15.908 4.021 3.297 I tried: $ gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -oall in which the index.ndx is $ [ atom ] $ 1 $ [ atom ] $ 19 But I was told: $ Available static index groups: $ Group 0 "atom" (1 atoms) $ Group 1 "atom" (1 atoms) $ Specify any number of selections for option 'select' $ (Position pairs to calculate distances for): $ (one per line, for status/groups, 'help' for help, Ctrl-D to end) How should I proceed with this? Is there a simple example example for the index.ndx? I could not find good answers at http://manual.gromacs.org/archive/5.0.3/online/ndx.html http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-distance.html Thank you. Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 To: "gromacs.org_gmx-users"; Subject: 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 -f equilibration.gro $ echo "r 1-442" "q" | gmx make_ndx -f equilibration.gro Thank you! -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 -f equilibration.gro $ echo "r 1-442" "q" | gmx make_ndx -f equilibration.gro Thank you! -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 a starting atom in the system (in my case the 41651th atom), it tries to change its conformation so as to yield lower "Epot" and "Fmax". Then it moves to the second atom, with "Dmax" distance from the first atom, and conducts the conformation change. It keeps moving around until the "Fmax" is lower than the "emtol", or the maximum steps has finished, or there is no more improvement. Please correct my understanding if possible. Basically, can we optimise the minimisation parameters simply based on the prompt (e.g. Dmax, Epot, Fmax, atom)? Cheng Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 Step=0, Dmax= 1.0e-02 nm, Epot= -1.92831e+06 Fmax= 1.63594e+03, atom= 41651 Step=1, Dmax= 1.0e-02 nm, Epot= -1.95056e+06 Fmax= 8.94326e+02, atom= 2170 Step=2, Dmax= 1.2e-02 nm, Epot= -1.98293e+06 Fmax= 4.67586e+02, atom= 73626 ... ... Step= 9998, Dmax= 2.3e-02 nm, Epot= -2.38236e+06 Fmax= 5.07179e+02, atom= 33278 Step= , Dmax= 1.1e-02 nm, Epot= -2.38236e+06 Fmax= 1.74071e+02, atom= 33278 Step=1, Dmax= 1.4e-02 nm, Epot= -2.38236e+06 Fmax= 2.22063e+02, atom= 33278 Energy minimization reached the maximum number of steps before the forces reached the requested precision Fmax < 10. writing lowest energy coordinates. Steepest Descents did not converge to Fmax < 10 in 10001 steps. Potential Energy = -2.3823640e+06 Maximum force = 2.2206276e+02 on atom 33278 Norm of force = 1.2667693e+00 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 "martini_v2.0_ions.itp") is shown in the system.top file. However, I found out that the above two lines could still work after removing the (#include "martini_v2.0_ions.itp"). Also, I can change "NA" and "CL" to any other names without any errors. So how the CG ions are reflected in the CG system? I think the CG ions are different from the all-atom ions, right? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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, 3 are non-polar and 4 are polar systems. Can I understand them in this way? (please do tell me any typos I have made) Can I also suggest if a more clear hierarchy (e.g. a table or tree structure) could be shown on the website? The current representation allocates "Particle definitions", "Amino Acids" and "Pure water solvent" at different webpages, which is okay. But if there is an overall breakdown, that would be much more straightforward to follow. (a search box would also be appreciated!) "forcefield.itp" (from martini_v2.2polIon folder) said: "It must be used with the refPOL.itp and refion.itp force field files for polarizable water and ions, respectively." But where are "refPOL.itp" and "refion.itp" files? 1) martini_v2.0.itp old non-polar version, not use 2) martini_v2.1.itp old non-polar version, not use 3) martini_v2.2.itp (updated: 05-12-2012) latest non-polar version -ff martini22 #include "martini_v2.2.itp" in the system.top non-polar water non-polar amino acid default ions 4) martini_v2.P.itp old polar version, not use 5) martini_v2.2P.itp (updated: 05-12-2012) default polar version -ff martini22p #include "martini_v2.2P.itp" in the system.top polar water polar amino acid default ions 6) martini_v2.2refP.itp (updated: 06-02-2017) refined polar version -ff martini22p #include "martini_v2.2refP.itp" in the system.top polar water & must with refPOL.itp polar amino acid default ions 7) martini_v2.2polIon.tar.gz (updated: 06-08-2018) Contains martini_v2.2refP.itp + NaCl refined polar version with refined ions -ff martini22p #include "forcefield.itp" (from martini_v2.2polIon folder) in the system.top polar water & must with refPOL.itp polar amino acid ions: ions.itp (from martini_v2.2polIon folder) martinize.py http://www.cgmartini.nl/images/tools/martinize/martinize-2.6/martinize.py non-polar water http://www.cgmartini.nl/images/applications/water/water.gro polar water http://www.cgmartini.nl/images/applications/water/polarize-water.gro non-polar amino acid http://www.cgmartini.nl/images/parameters/ITP/martini_v2.2_aminoacids.itp polar amino acid http://www.cgmartini.nl/images/parameters/ITP/martini_v2.2P_aminoacids.itp default ions http://www.cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 "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 you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to set the inter-chain disulfind bond in martini?
Dear Peter,
Thank you, I find the answer now. Sorry I was using a pdb that the SS length is
too long to form the SS bond. After changing to a correct one, I got the
solution.
I think, if we have more than one chain, we MUST use "-merge" option, so that
the interchain SS bond 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"<272699...@qq.com>;
Date: Tue, Jan 29, 2019 11:03 PM
To: "gromacs.org_gmx-users";
Subject: 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 will only generate four intrachain disulfide bonds, without
the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H
prompt:
$ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying
closer than 0.2200 nm
$ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG',
'CYS', 88, 'L') (0.204094 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG',
'CYS', 194, 'L') (0.204489 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG',
'CYS', 434, 'H') (0.203603 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG',
'CYS', 414, 'H') (0.204830 nm)
I can see the four disulfide bonds information is reflected in the [
constraints ] section of "Protein_L+Protein_H.itp" file:
$ 45 191 1 0.24000 ; Cys-bonds/special link
$ 294 431 1 0.24000 ; Cys-bonds/special link
$ 475 947 1 0.24000 ; Cys-bonds/special link
$ 778 900 1 0.24000 ; Cys-bonds/special link
So how to also ensure the intactness of the interchain disulfide bond?
You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide
Thank you!
Yours sincerely
Cheng
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[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 will only generate four intrachain disulfide bonds, without
the interchain one:
$ python martinize.py -f protein.pdb -o system.top -x protein-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 -cys auto -merge L,H
prompt:
$ INFO Checking for cystine bridges, based on sulphur (SG) atoms lying
closer than 0.2200 nm
$ INFO Detected SS bridge between ('SG', 'CYS', 23, 'L') and ('SG',
'CYS', 88, 'L') (0.204094 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 134, 'L') and ('SG',
'CYS', 194, 'L') (0.204489 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 214, 'L') and ('SG',
'CYS', 434, 'H') (0.203603 nm)
$ INFO Detected SS bridge between ('SG', 'CYS', 358, 'H') and ('SG',
'CYS', 414, 'H') (0.204830 nm)
I can see the four disulfide bonds information is reflected in the [
constraints ] section of "Protein_L+Protein_H.itp" file:
$ 45 191 1 0.24000 ; Cys-bonds/special link
$ 294 431 1 0.24000 ; Cys-bonds/special link
$ 475 947 1 0.24000 ; Cys-bonds/special link
$ 778 900 1 0.24000 ; Cys-bonds/special link
So how to also ensure the intactness of the interchain disulfide bond?
You can find my files at
https://github.com/lanselibai/martini/tree/master/20190129_disulfide
Thank you!
Yours sincerely
Cheng
--
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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 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 ASP and GLU. Now I want to change the protonation states based on a particular pH as determined by pdb2pqr server. 1) For backbones, if my N-terminus residue is MET: 1Qd 1 METBB 1 1. ; C 2C5 1 MET SC1 2 0. ; C based on "martini_v2.2P_aminoacids.itp" for MET: ;id type resnr residu atom cgnr charge 1 P5 1 MET BB 1 0 2 C5 1 MET SC12 0 should I change to this? 1P5 1 METBB 1 0. ; C 2C5 1 MET SC1 2 0. ; C 2) For side chains, e.g. GLU 362P5 165 GLUBB 362 0. ; C 363Qa 165 GLU SC1 363 -1. ; C if I do not want GLU to be negatively charged, based on "martini_v2.2P_aminoacids.itp" for GLU neutral form: ;id type resnr residu atom cgnr charge 1 P5 1 GLU0BB 1 0 2 P1 1 GLU0SC12 0 should I change to this? 362P5 165 GLU0 BB 362 0. ; C 363P1 165 GLU0 SC1 363 0. ; C Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 ASP and GLU. Now I want to change the protonation states based on a particular pH as determined by pdb2pqr server. 1) For backbones, if my N-terminus residue is MET: 1Qd 1 METBB 1 1. ; C 2C5 1 MET SC1 2 0. ; C based on "martini_v2.2P_aminoacids.itp" for MET: ;id type resnr residu atom cgnr charge 1 P5 1 MET BB 1 0 2 C5 1 MET SC12 0 should I change to this? 1P5 1 METBB 1 0. ; C 2C5 1 MET SC1 2 0. ; C 2) For side chains, e.g. GLU 362P5 165 GLUBB 362 0. ; C 363Qa 165 GLU SC1 363 -1. ; C if I do not want GLU to be negatively charged, based on "martini_v2.2P_aminoacids.itp" for GLU neutral form: ;id type resnr residu atom cgnr charge 1 P5 1 GLU0BB 1 0 2 P1 1 GLU0SC12 0 should I change to this? 362P5 165 GLU0 BB 362 0. ; C 363P1 165 GLU0 SC1 363 0. ; C Thank you! Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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: What is the difference of using "system" and separating groups for "tc-grps"? In the mdp file, I am using "tcoupl = v-rescale". Is there a difference between using "system" and separating groups for "tc-grps"? e.g. ; using "system": tc-grps = system tau-t= 1.0 ref-t= 335 ; using separating groups: tc-grps = Protein W NA CL tau-t= 1.0 1.0 1.0 1.0 ref-t= 335 335 335 335 Thank you! -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters
Dear All, (hope this message can be put under the original thread) I solved this problem. The reason is, I was trying to fill the system with water then minimise it, which is not good. The better way is, prepare a waterbox that is even larger than the system box. Then minimise that water 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: "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters Dear Fotis and Peter, Thank you very much for the help. Fotis, Can I modify the mdp file to use "soft" potential modifier, how to do that? I think my problem is not the first reason (i.e. something wrong with the system structure or topology), because the potential is decreasing for the minimization step after inserting 10 protein molecules https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization%20after%20insert%2010%20proteins.jpg $ Steepest Descents converged to machine precision in 4251 steps, $ but did not reach the requested Fmax < 1. $ Potential 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: Tue, Jan 22, 2019 05:58 AM To: "gromacs.org_gmx-users"; Subject: Re: "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to 100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100", i.e. outputting dozens of pdb files before the "LINCS warnings". Then I looked at the edr files. The potential in "emtol = 1000" and "emtol = 100" runs were actually converging https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png My understanding for the "LINCS warnings" is, the system is not stable. But why the potential is still converging? Do I need to adjust the "lincs warning threshold", or "set the environment variable GMX_MAXCONSTRWARN to -1"? How to do that? Is there a "standard" mdp file for minimization for a coarse-grained system with 10 proteins in water? I 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-users"; Subject: "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 My procedure is 1) A single CG-protein was firstly minimized in vacuum, no problem 2) Then 10 of this protein were inserted to a box, followed by a minimization. It "stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step." So I think this minimization is also successful. 3) The system was then solvated by $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro -p system.top 4) Then the solvated system is minimized by $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top -o system-min-solvent.tpr $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro PDB structures were outputted from step 327 to step 710, and it stopped due to the "LINCS warnings". The "minimization_solvate.mdp" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp The "system-min-solvent.log" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log So I think the system with 10 proteins in vacuum is okay (right?). But when CG-water is added, it got problem? How to modify my system? Let me know if you need other information. Thank you. Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters
Dear Fotis and Peter, Thank you very much for the help. Fotis, Can I modify the mdp file to use "soft" potential modifier, how to do that? I think my problem is not the first reason (i.e. something wrong with the system structure or topology), because the potential is decreasing for the minimization step after inserting 10 protein molecules https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization%20after%20insert%2010%20proteins.jpg $ Steepest Descents converged to machine precision in 4251 steps, $ but did not reach the requested Fmax < 1. $ Potential 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: Tue, Jan 22, 2019 05:58 AM To: "gromacs.org_gmx-users"; Subject: Re: "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to 100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100", i.e. outputting dozens of pdb files before the "LINCS warnings". Then I looked at the edr files. The potential in "emtol = 1000" and "emtol = 100" runs were actually converging https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png My understanding for the "LINCS warnings" is, the system is not stable. But why the potential is still converging? Do I need to adjust the "lincs warning threshold", or "set the environment variable GMX_MAXCONSTRWARN to -1"? How to do that? Is there a "standard" mdp file for minimization for a coarse-grained system with 10 proteins in water? I 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-users"; Subject: "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 My procedure is 1) A single CG-protein was firstly minimized in vacuum, no problem 2) Then 10 of this protein were inserted to a box, followed by a minimization. It "stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step." So I think this minimization is also successful. 3) The system was then solvated by $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro -p system.top 4) Then the solvated system is minimized by $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top -o system-min-solvent.tpr $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro PDB structures were outputted from step 327 to step 710, and it stopped due to the "LINCS warnings". The "minimization_solvate.mdp" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp The "system-min-solvent.log" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log So I think the system with 10 proteins in vacuum is okay (right?). But when CG-water is added, it got problem? How to modify my system? Let me know if you need other information. Thank you. Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters
I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to 100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100", i.e. outputting dozens of pdb files before the "LINCS warnings". Then I looked at the edr files. The potential in "emtol = 1000" and "emtol = 100" runs were actually converging https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png My understanding for the "LINCS warnings" is, the system is not stable. But why the potential is still converging? Do I need to adjust the "lincs warning threshold", or "set the environment variable GMX_MAXCONSTRWARN to -1"? How to do that? Is there a "standard" mdp file for minimization for a coarse-grained system with 10 proteins in water? I 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-users"; Subject: "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 My procedure is 1) A single CG-protein was firstly minimized in vacuum, no problem 2) Then 10 of this protein were inserted to a box, followed by a minimization. It "stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step." So I think this minimization is also successful. 3) The system was then solvated by $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro -p system.top 4) Then the solvated system is minimized by $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top -o system-min-solvent.tpr $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro PDB structures were outputted from step 327 to step 710, and it stopped due to the "LINCS warnings". The "minimization_solvate.mdp" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp The "system-min-solvent.log" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log So I think the system with 10 proteins in vacuum is okay (right?). But when CG-water is added, it got problem? How to modify my system? Let me know if you need other information. Thank you. Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 My procedure is 1) A single CG-protein was firstly minimized in vacuum, no problem 2) Then 10 of this protein were inserted to a box, followed by a minimization. It "stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step." So I think this minimization is also successful. 3) The system was then solvated by $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro -p system.top 4) Then the solvated system is minimized by $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top -o system-min-solvent.tpr $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro PDB structures were outputted from step 327 to step 710, and it stopped due to the "LINCS warnings". The "minimization_solvate.mdp" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp The "system-min-solvent.log" is here https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log So I think the system with 10 proteins in vacuum is okay (right?). But when CG-water is added, it got problem? How to modify my system? Let me know if you need other information. Thank you. Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 is not automatically done? The prompt also shows "0" for "Number of SOL molecules": Generating solvent configuration Will generate new solvent configuration of 3x3x3 boxes Solvent box contains 4435 atoms in 4435 residues Removed 1235 solvent atoms due to solvent-solvent overlap Removed 1286 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: W ( 1 atoms): 768 residues Generated solvent containing 768 atoms in 768 residues Writing generated configuration to waterbox.gro Output configuration contains 2304 atoms in 896 residues Volume : 421.875 (nm^3) Density: 639.416 (g/l) Number of SOL molecules: 0 Processing topology Back Off! I just backed up dppc.top to ./#dppc.top.1# -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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" 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 Maximum force = 9.8130465e+00 on atom 405 Norm of force = 1.5696382e+00 My mdp file is: integrator = steep nsteps = 1 nstxout = 0 nstfout = 0 nstlog = 100 cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 coulombtype = reaction-field rcoulomb = 1.1 epsilon_r= 15; 2.5 (with polarizable water) epsilon_rf = 0 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 Maximum force = 9.8130465e+00 on atom 405 Norm of force = 1.5696382e+00 My mdp file is: integrator = steep nsteps = 1 nstxout = 0 nstfout = 0 nstlog = 100 cutoff-scheme= Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 coulombtype = reaction-field rcoulomb = 1.1 epsilon_r= 15; 2.5 (with polarizable water) epsilon_rf = 0 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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: "gromacs.org_gmx-users"; Subject: 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 as the file for "-r"? I tried both, and both can work without errors. But which one is more logically correct? I think the CG.pdb should definitely work. But why AllAtom.pdb is still okay? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?
Hi Mark, Thank you for your help! Sorry I was totally confused. I thought I should delete the "define = -DPOSRES" option and use "-r target.pdb". Now I understand that. I should ) still keep the "define = -DPOSRES" in the mdp file ) still keep the "[ position_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"<272699...@qq.com>; Date: Wed, Jan 16, 2019 09:51 PM To: "gromacs.org_gmx-users"; Subject: 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 atoms in the "target.pdb" will be restrained. My coarse-grained pdb looks like this: ATOM 1 BB PRO A 1 -26.587 30.562 25.782 1.00 0.00 B ATOM 2 SC1 PRO A 1 -28.091 28.941 24.961 1.00 0.00 S ATOM 3 BB GLN A 2 -25.999 30.486 29.213 1.00 0.00 B ATOM 4 SC1 GLN A 2 -25.071 33.603 31.302 1.00 0.00 S ATOM 5 BB ILE A 3 -23.280 28.735 30.757 1.00 0.00 B ATOM 6 SC1 ILE A 3 -23.796 26.273 28.833 1.00 0.00 S ... ... ATOM201 BB ASN A 98 -16.655 34.258 30.350 1.00 0.00 B ATOM202 SC1 ASN A 98 -18.546 35.721 27.829 1.00 0.00 S ATOM203 BB PHE A 99 -15.212 36.640 33.153 1.00 0.00 B ATOM204 SC1 PHE A 99 -13.341 34.692 33.167 1.00 0.00 S ATOM205 SC2 PHE A 99 -11.471 35.716 34.112 1.00 0.00 S ATOM206 SC3 PHE A 99 -10.740 34.794 32.402 1.00 0.00 S The "position_restraints" looks like this in the protein.itp file: (you can see only the backbone atom ID is listed, i.e. 1, 3, 5 ... 201, 203) #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FCPOSRES_FC ... ... 2011POSRES_FCPOSRES_FCPOSRES_FC 2031POSRES_FCPOSRES_FCPOSRES_FC #endif -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 atoms in the "target.pdb" will be restrained. My coarse-grained pdb looks like this: ATOM 1 BB PRO A 1 -26.587 30.562 25.782 1.00 0.00 B ATOM 2 SC1 PRO A 1 -28.091 28.941 24.961 1.00 0.00 S ATOM 3 BB GLN A 2 -25.999 30.486 29.213 1.00 0.00 B ATOM 4 SC1 GLN A 2 -25.071 33.603 31.302 1.00 0.00 S ATOM 5 BB ILE A 3 -23.280 28.735 30.757 1.00 0.00 B ATOM 6 SC1 ILE A 3 -23.796 26.273 28.833 1.00 0.00 S ... ... ATOM201 BB ASN A 98 -16.655 34.258 30.350 1.00 0.00 B ATOM202 SC1 ASN A 98 -18.546 35.721 27.829 1.00 0.00 S ATOM203 BB PHE A 99 -15.212 36.640 33.153 1.00 0.00 B ATOM204 SC1 PHE A 99 -13.341 34.692 33.167 1.00 0.00 S ATOM205 SC2 PHE A 99 -11.471 35.716 34.112 1.00 0.00 S ATOM206 SC3 PHE A 99 -10.740 34.794 32.402 1.00 0.00 S The "position_restraints" looks like this in the protein.itp file: (you can see only the backbone atom ID is listed, i.e. 1, 3, 5 ... 201, 203) #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FCPOSRES_FC ... ... 2011POSRES_FCPOSRES_FCPOSRES_FC 2031POSRES_FCPOSRES_FCPOSRES_FC #endif -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 as the file for "-r"? I tried both, and both can work without errors. But which one is more logically correct? I think the CG.pdb should definitely work. But why AllAtom.pdb is still okay? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?
Thank you Mark! The "Protein_A.itp" is obtained by: python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -dssp ./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 So the "Protein_A.itp" has the restraints in the "1UBQ-CG.pdb". So I should use "-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 To: "gromacs.org_gmx-users"; Subject: Re: How to use "define = -DPOSRES" in Gromacs 2018? Thank you Mark! Sorry, I do not have a "targetcoords.gro" for the grompp. I was trying to use "gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o minimization.tpr", and the "system.top" has a line of " #include "Protein_A.itp" ", 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-users"; Subject: 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_FCPOSRES_FC .. 1621POSRES_FCPOSRES_FCPOSRES_FC 1631POSRES_FCPOSRES_FCPOSRES_FC #endif The Martini protein tutorial said: specify "define = -DPOSRES" in the mdp file for "gmx grompp". However, adding "define = -DPOSRES" to the mdp file causes the error: Fatal error: Cannot find position restraint file restraint.gro (option -r). >From GROMACS-2018, you need to specify the position restraint coordinate files explicitly to avoid mistakes, although you can still use the same file as you specify for the -c option. The tutorial uses Gromacs 5, but I am using Gromacs 2018. Is this the problem for that? How can I trigger those restraints in "Protein_A.itp" file using Gromacs 2018? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?
Thank you Mark! Sorry, I do not have a "targetcoords.gro" for the grompp. I was trying to use "gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o minimization.tpr", and the "system.top" has a line of " #include "Protein_A.itp" ", 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-users"; Subject: 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_FCPOSRES_FC .. 1621POSRES_FCPOSRES_FCPOSRES_FC 1631POSRES_FCPOSRES_FCPOSRES_FC #endif The Martini protein tutorial said: specify "define = -DPOSRES" in the mdp file for "gmx grompp". However, adding "define = -DPOSRES" to the mdp file causes the error: Fatal error: Cannot find position restraint file restraint.gro (option -r). >From GROMACS-2018, you need to specify the position restraint coordinate files explicitly to avoid mistakes, although you can still use the same file as you specify for the -c option. The tutorial uses Gromacs 5, but I am using Gromacs 2018. Is this the problem for that? How can I trigger those restraints in "Protein_A.itp" file using Gromacs 2018? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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_FCPOSRES_FC .. 1621POSRES_FCPOSRES_FCPOSRES_FC 1631POSRES_FCPOSRES_FCPOSRES_FC #endif The Martini protein tutorial said: specify "define = -DPOSRES" in the mdp file for "gmx grompp". However, adding "define = -DPOSRES" to the mdp file causes the error: Fatal error: Cannot find position restraint file restraint.gro (option -r). >From GROMACS-2018, you need to specify the position restraint coordinate files explicitly to avoid mistakes, although you can still use the same file as you specify for the -c option. The tutorial uses Gromacs 5, but I am using Gromacs 2018. Is this the problem for that? How can I trigger those restraints in "Protein_A.itp" file using Gromacs 2018? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 To: "gromacs.org_gmx-users"; Subject: Re: Why pdb2gmx could not accept tip4pd as the water model? I think using "-water tip4pd" will always cause errors, without allowing me to select the forcefield. I also put the ff directory to my launching folder, but still the same problem. Simply using "-water tip4p" will allow me to select the forcefield. But I want to use tip4pd, not tip4p. The below is the error message. GROMACS: gmx pdb2gmx, version 2018.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/lanselibai/Cheng/gromacs/20190110_a99SBdisp Command line: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water tip4pd -inter -ignh -merge interactive --- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function:void gmx::CommandLineParser::parse(int*, char**) Error in user input: 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 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. -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:12 AM To: "gromacs.org_gmx-users"; Subject: 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 cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
I think using "-water tip4pd" will always cause errors, without allowing me to select the forcefield. I also put the ff directory to my launching folder, but still the same problem. Simply using "-water tip4p" will allow me to select the forcefield. But I want to use tip4pd, not tip4p. The below is the error message. GROMACS: gmx pdb2gmx, version 2018.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/lanselibai/Cheng/gromacs/20190110_a99SBdisp Command line: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water tip4pd -inter -ignh -merge interactive --- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function:void gmx::CommandLineParser::parse(int*, char**) Error in user input: 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 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. -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:12 AM To: "gromacs.org_gmx-users"; Subject: 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 cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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. ------ Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:12 AM To: "gromacs.org_gmx-users"; Subject: 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 cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to install a new force-field?
Hi Justin, I can use the new force field if I put it under the working directory. You also mentioned that I can put it under $GMXLIB. However, I could not find it when the ff is put at /home/lanselibai/Cheng/gromacs-2018.1/build/src/gromacs/gmxlib/charmm36-nov2018.ff So what 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 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 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"<272699...@qq.com>; Date: Sun, Dec 23, 2018 10:38 PM To: "gromacs.org_gmx-users"; Subject: 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 download them? At this website, http://www.gromacs.org/Downloads/User_contributions/Force_fields I could not find a99SB-disp and CHARMM36m. 2) How to install them? Is there a step-by-step instruction for the installation? Thank you. Yours sincerely Cheng CHARMM36m: an improved force field for folded and intrinsically disordered proteins https://www.nature.com/articles/nmeth.4067 a99SB-disp: Developing a molecular dynamics force field for both folded and disordered protein states https://www.pnas.org/content/115/21/E4758 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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 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"<272699...@qq.com>; Date: Sun, Dec 23, 2018 10:38 PM To: "gromacs.org_gmx-users"; Subject: 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 download them? At this website, http://www.gromacs.org/Downloads/User_contributions/Force_fields I could not find a99SB-disp and CHARMM36m. 2) How to install them? Is there a step-by-step instruction for the installation? Thank you. Yours sincerely Cheng CHARMM36m: an improved force field for folded and intrinsically disordered proteins https://www.nature.com/articles/nmeth.4067 a99SB-disp: Developing a molecular dynamics force field for both folded and disordered protein states https://www.pnas.org/content/115/21/E4758 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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"<272699...@qq.com>; Date: Sun, Dec 23, 2018 10:38 PM To: "gromacs.org_gmx-users"; Subject: 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 download them? At this website, http://www.gromacs.org/Downloads/User_contributions/Force_fields I could not find a99SB-disp and CHARMM36m. 2) How to install them? Is there a step-by-step instruction for the installation? Thank you. Yours sincerely Cheng CHARMM36m: an improved force field for folded and intrinsically disordered proteins https://www.nature.com/articles/nmeth.4067 a99SB-disp: Developing a molecular dynamics force field for both folded and disordered protein states https://www.pnas.org/content/115/21/E4758 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 download them? At this website, http://www.gromacs.org/Downloads/User_contributions/Force_fields I could not find a99SB-disp and CHARMM36m. 2) How to install them? Is there a step-by-step instruction for the installation? Thank you. Yours sincerely Cheng CHARMM36m: an improved force field for folded and intrinsically disordered proteins https://www.nature.com/articles/nmeth.4067 a99SB-disp: Developing a molecular dynamics force field for both folded and disordered protein states https://www.pnas.org/content/115/21/E4758 -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] chain separator issue for the "gmx do_dssp": do NOT need to provide a "ss.map" file
Also, can the "map file format" page be updated with "chain separator"? http://manual.gromacs.org/online/map.html 9 ~ Coil 1 1 1 E B-Sheet 1 0 0 B B-Bridge 0 0 0 S Bend 0 0.5 0 T Turn 1 1 0 H A-Helix 0 0 1 I 5-Helix 0.5 0 0.5 G 3-Helix 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@maillist.sys.kth.se>;"ZHANG Cheng"<272699...@qq.com>; Subject: 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 the default "ss.map" file automatically, and the ss.xpm file will have a line of "" as the chain separator. I created my own ss.map file based on http://manual.gromacs.org/online/map.html, and got the "~~" as chain separator, which is the same as coils. So do not do this. -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 the default "ss.map" file automatically, and the ss.xpm file will have a line of "" as the chain separator. I created my own ss.map file based on http://manual.gromacs.org/online/map.html, and got the "~~" as chain separator, which is the same as coils. So do not do this. -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 show in the beginning or
between the two chains?
(Sorry, I asked this question about chain separator before. But if the last
residue shows first, it is possible that the chain separator is between the two
chains. But I really want to confirm that. Or how can I get contact with the
author who wrote the "gmx do_dssp"?)
I found the original post for the source code at
http://repo.or.cz/gromacs.git/commit/5e4dd0a15de15237ec34ac287dca8e0aa01adb40
Can I ask how to use the "repo.or.cz" website? I am not sure how to register it.
I also emailed the author Carsten, but have not got reply.
Thank you.
Yours sincerely
Cheng
First a few lines:
---
/* XPM */
/* Created by: */
/*:-) GROMACS - gmx do_dssp, VERSION 5.1.1 (-: */
/* */
/* Executable: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx */
/* Data prefix: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2 */
/* Command line: */
/* 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 */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title: "Secondary structure" */
/* legend: "" */
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"1064 443 8 1",
"~ c #FF " /* "Coil" */,
"E c #FF " /* "B-Sheet" */,
"B c #00 " /* "B-Bridge" */,
"S c #00 " /* "Bend" */,
"T c #00 " /* "Turn" */,
"H c #FF " /* "A-Helix" */,
"G c #FF00FF " /* "3-Helix" */,
"I c #FF9900 " /* "5-Helix" */,
--
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[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 question about chain separator before. But if the last
residue shows first, it is possible that the chain separator is between the two
chains. But I really want to confirm that. Or how can I get contact with the
author who wrote the "gmx do_dssp"?)
Thank you.
Yours sincerely
Cheng
First a few lines:
---
/* XPM */
/* Created by: */
/*:-) GROMACS - gmx do_dssp, VERSION 5.1.1 (-: */
/* */
/* Executable: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx */
/* Data prefix: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2 */
/* Command line: */
/* 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 */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title: "Secondary structure" */
/* legend: "" */
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"1064 443 8 1",
"~ c #FF " /* "Coil" */,
"E c #FF " /* "B-Sheet" */,
"B c #00 " /* "B-Bridge" */,
"S c #00 " /* "Bend" */,
"T c #00 " /* "Turn" */,
"H c #FF " /* "A-Helix" */,
"G c #FF00FF " /* "3-Helix" */,
"I c #FF9900 " /* "5-Helix" */,
--
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[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 sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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: 'Structure','Coil','B-Sheet','B-Bridge','Bend','Turn','A-Helix','3-Helix','5-Helix' I ran the command for different proteins. It surprised me that the last '5-Helix' randomly displayed in the scount.xvg. Maybe some proteins did not have the '5-Helix', but why not just show them as 0? Can this be improved? Because I am using a script to read the scount.xvg files, so I want all the files have the same format. Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why "do_dssp" gives one more residue?
Dear Justin,
Thank you. But it does not make sense to me. Do you know if separator line is
always all the ~ ? If the separator line is following the 214th residue, the
215th residue should be the separator line, but why the 215th residue contains
the secondary structure?
You can find my files at
https://1drv.ms/f/s!AjIs-W_id1LzpOsT2Dktn9hIO7-eNA
If you use a text editor,
The 214th residue: line 248
The 215th residue: line 249
The pdb file (bfac.pdb) after the simulation is also in the link (without the
chain ID).
The original pdb I use contains two chains. After running "gmx pdb2gmx -f
protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge
interactive", the two chains are merged to keep the inter-chain disulfide bond,
and also the chain ID has been lost since then.
Thank you.
Yours sincerely
Cheng
-- 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 numbering is:
1-214: first chain
215-442: second chain
However, for the secondary structure codes:
214th:
"TTSTSSSTSSSTTSTSS~SSSSSSTSSSTSTTTSTSTSTT~SS~SSSTSTTTSSTTTSSTSSTTTSSGSTTSTSSSTSSTSSTTSSTSTTSSSTSSTTTTTEEBSSEBSSTSSTSEESTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTTESET~~~SSS~SSS~~S~",
215th:
"TTST~~~TSSSTTSTSSSSSTSSSTSTTTSTSTSTT~~~TSTTT~STTTSSTSSTTTSSGSTTSTS~S~SSSTSSTSSTTTSTTSSTSTTSSSTSSTTTTTSTSSTTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTT~SSS~S",
442th:
"~~~B~~BBB~BB~BBB~B~~~B~~BT~B~B~~B",
443th:
"~"
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.sys.kth.se>;"ZHANG
Cheng"<272699...@qq.com>;
Subject: 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 443.
Can I ask why is that? Should I just ignore the 443th data?
Yours sincerely
Cheng
Here is some content copied from the ss.xpm file:
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443 8 1",
... ...
/* y-axis: 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437
438 439 440 441 442 443 */
--
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Re: [gmx-users] Why "do_dssp" gives one more residue?
Dear Qinghua,
Yes, exactly! But the numbering is:
1-214: first chain
215-442: second chain
However, for the secondary structure codes:
214th:
"TTSTSSSTSSSTTSTSS~SSSSSSTSSSTSTTTSTSTSTT~SS~SSSTSTTTSSTTTSSTSSTTTSSGSTTSTSSSTSSTSSTTSSTSTTSSSTSSTTTTTEEBSSEBSSTSSTSEESTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTTESET~~~SSS~SSS~~S~",
215th:
"TTST~~~TSSSTTSTSSSSSTSSSTSTTTSTSTSTT~~~TSTTT~STTTSSTSSTTTSSGSTTSTS~S~SSSTSSTSSTTTSTTSSTSTTSSSTSSTTTTTSTSSTTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTT~SSS~S",
442th:
"~~~B~~BBB~BB~BBB~B~~~B~~BT~B~B~~B",
443th:
"~"
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.sys.kth.se>;"ZHANG
Cheng"<272699...@qq.com>;
Subject: 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 443.
Can I ask why is that? Should I just ignore the 443th data?
Yours sincerely
Cheng
Here is some content copied from the ss.xpm file:
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443 8 1",
... ...
/* y-axis: 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437
438 439 440 441 442 443 */
--
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[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 443.
Can I ask why is that? Should I just ignore the 443th data?
Yours sincerely
Cheng
Here is some content copied from the ss.xpm file:
/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443 8 1",
... ...
/* y-axis: 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437
438 439 440 441 442 443 */
--
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[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 pdb file? Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can I put b-factor into xtc file?
Thank you Mark for this fascinating tng format. I think I could not modify it using C/C++ at this moment. For your "easier approach", do you mean I can convert xtc to pdb frame with b-factor assigned, if I provide the b-factor file? How to do this? -- 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 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 you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 Gromacs has other tools (e.g. STRIDE) for secondary structure analysis? Now I am using the VMD-Timeline tool, which uses the STRIDE http://webclu.bio.wzw.tum.de/stride/ Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 dropping in the gyration radius, from ~2.6 nm to ~2.2 nm in 50 ns. Can I ask if this phenomenon is common? Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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: "ZHANG Cheng";<272699...@qq.com>; Date: Sat, Jan 20, 2018 00:45 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: 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 commands to delete all of them in one go, : rm md_0_1.e* rm md_0_1.o* rm md_0_1.pe* rm md_0_1.po* I thought the checkpoint information is only stored in md_0_1.cpt, md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not delete. However, after deleting all the log files, and then started a new run, I was told: Fatal error: File appending requested, but 1 of the 4 output files are not present or are named differently So it seems that the checkpoint information is also in one of those md_0_1.e, md_0_1.o, md_0_1.pe, md_0_1.po files? Thank you. -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 commands to delete all of them in one go, : rm md_0_1.e* rm md_0_1.o* rm md_0_1.pe* rm md_0_1.po* I thought the checkpoint information is only stored in md_0_1.cpt, md_0_1_prev.cpt and some files like md_0_1_step47660830.cpt, which I did not delete. However, after deleting all the log files, and then started a new run, I was told: Fatal error: File appending requested, but 1 of the 4 output files are not present or are named differently So it seems that the checkpoint information is also in one of those md_0_1.e, md_0_1.o, md_0_1.pe, md_0_1.po files? Thank you. -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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:Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, Thank you very much! The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded? e.g. 1.467/2.767 1.824/2.757 1.901/2.736 ... ... ------ 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 surface area using "gmx sasa"? Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.9841.901 ... ... So my understanding is ) 1st column is the time ) 2nd column is the sasa of the whole protein ) 3rd column is the sasa of the particular group Thank you for that. But may I ask 1) if it is possible to calculate the fraction for a particular group in this way: (sasa of the state in the xtc file)/(sasa when that group is fully unfolded) Because a big buried residue may have similar sasa compared to a small exposed residue, so the "absolute" sasa of each residue could not reflect their buried extents individually. 2) When I do not use -surface and -output, but use echo: echo 1|gmx sasa -f md_0_1.xtc -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";<272699...@qq.com>; Date: Tue, Jan 16, 2018 07:19 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: 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.kth.se>; Subject: Re:Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? 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 -- 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 Justin, Thank you very much! The legend is "Total" for the command without -surface and -output. So I feel like if I do a division for the last columns from those two commands, I can just get the fraction of folded/unfolded? e.g. 1.467/2.767 1.824/2.757 1.901/2.736 ... ... -- 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 surface area using "gmx sasa"? Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.9841.901 ... ... So my understanding is ) 1st column is the time ) 2nd column is the sasa of the whole protein ) 3rd column is the sasa of the particular group Thank you for that. But may I ask 1) if it is possible to calculate the fraction for a particular group in this way: (sasa of the state in the xtc file)/(sasa when that group is fully unfolded) Because a big buried residue may have similar sasa compared to a small exposed residue, so the "absolute" sasa of each residue could not reflect their buried extents individually. 2) When I do not use -surface and -output, but use echo: echo 1|gmx sasa -f md_0_1.xtc -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";<272699...@qq.com>; Date: Tue, Jan 16, 2018 07:19 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: 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.kth.se>; Subject: Re:Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? 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 -- 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"? 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 exposure extent of a residue. For example, a buried big residue may
Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
Hi Justin, Thank you very much. So I tried: gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface 'group 0' -output 'group 1' And got: 0.000 206.8651.467 0.100 232.4501.824 0.200 225.9841.901 ... ... So my understanding is ) 1st column is the time ) 2nd column is the sasa of the whole protein ) 3rd column is the sasa of the particular group Thank you for that. But may I ask 1) if it is possible to calculate the fraction for a particular group in this way: (sasa of the state in the xtc file)/(sasa when that group is fully unfolded) Because a big buried residue may have similar sasa compared to a small exposed residue, so the "absolute" sasa of each residue could not reflect their buried extents individually. 2) When I do not use -surface and -output, but use echo: echo 1|gmx sasa -f md_0_1.xtc -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";<272699...@qq.com>; Date: Tue, Jan 16, 2018 07:19 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: 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.kth.se>; Subject: Re:Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? 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 -- 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"? 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 exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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.kth.se>; Subject: Re:Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? 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 -- 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"? 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 exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
Hi Justin, thank you very much. Sorry I still do not fully understand. I have an index file, in which the group 0 is all the residue atoms of the protein, group 1 is the first residue atoms. I want to calculate the sasa fraction of the residue 1. The fraction means: the sasa at folded state divided by the sasa when the residue is fully unfolded. So as you said, "two selections, one for the surface, the other for what is output". ) The manual says: "-surface should always consist of all non-solvent atoms in the system", so in my case it should be group 0, right? ) The manual also says: "-output can specify additional selections, which should be subsets of the calculation group", so in my case, it should be group 1, right? so I tried: echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns -surface -output And got error message: Error in user input: Invalid selection '0 1 ' Near '1' syntax error I also tried "echo 1 0", and got the similar error: Error in user input: Invalid selection '1 0 ' Near '0' syntax error Can you please help me? Thank you very much! ------ Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Tue, Jan 16, 2018 04:52 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: Can I get the fraction of solvent accessible surface area using "gmx sasa"? 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 -- 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"? 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 exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?
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 -- 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"? 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 exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 exposure extent of a residue. For example, a buried big residue may have similar sasa as an exposed small residue. Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] What is the most reliable way to run repeats for reproducibility?
Hi Mark, Thank you very much. ) For the link you provide, I think I could not manipulate most of the computer resources, as I submit my jobs to our cluster, and the jobs are distributed to different available cores randomly. ) For "random seed" of velocity, I found here and I enabled this option: gen_vel = yes http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html So does it mean that it is better to use the same em.tpr and run different NVT,NPT,etc. for different repeats, so as to initialise it with different velocities? ) How the "natural chaotic divergence during equilibration" is reflected at which step? The link says: "The Central Limit Theorem tells us that in the case of infinitely long simulation all observables converge to their equilibrium values". But I think this "equilibrium" is not practical for protein in MD. For example, if I am running a protein at 370K, ultimately it will unfold, like boiling an egg in water, it takes 10 min. But in MD, the time scale is way more shorter, i.e. usually a few hundred ns scale. We could "never" see the proteins converges within that short period. So my understanding about "equilibrium" is the equilibration for temperature/pressure/density, but not the protein itself. Is that correct? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html http://www.bevanlab.biochem.vt.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.org_gmx-users@maillist.sys.kth.se>; Subject: 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 ?? NPT ?? md_0_1.tpr?? production MD ) repeat 2: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD ) repeat 3: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD .. The 2nd way: all starting from the same md_0_1.tpr and use it for different production MD: ) repeat 1: same em.tpr ?? same NVT ?? same NPT ?? same md_0_1.tpr?? production MD ) repeat 2: same md_0_1.tpr?? production MD ) repeat 3: same md_0_1.tpr?? production MD .. The 3rd way: all starting from the same check point file within the production run and use it for the rest of the production MD: ) repeat 1: same em.tpr ?? same NVT ?? same NPT ?? same md_0_1.tpr?? same production MD for 50 ns ?? same .cpt file ?? production MD for another 200 ns ) repeat 2: same .cpt file ?? production MD for another 200 ns ) repeat 3: same .cpt file ?? production MD for another 200 ns .. Of course, the 3rd way is easier. But does it mean it may not cover enough conformations, as they tend to be more resembled from each other than the 1st approach? Is there a standard way to handle the repeats? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 ?? NPT ?? md_0_1.tpr?? production MD ) repeat 2: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD ) repeat 3: same em.tpr ?? NVT ?? NPT ?? md_0_1.tpr?? production MD .. The 2nd way: all starting from the same md_0_1.tpr and use it for different production MD: ) repeat 1: same em.tpr ?? same NVT ?? same NPT ?? same md_0_1.tpr?? production MD ) repeat 2: same md_0_1.tpr?? production MD ) repeat 3: same md_0_1.tpr?? production MD .. The 3rd way: all starting from the same check point file within the production run and use it for the rest of the production MD: ) repeat 1: same em.tpr ?? same NVT ?? same NPT ?? same md_0_1.tpr?? same production MD for 50 ns ?? same .cpt file ?? production MD for another 200 ns ) repeat 2: same .cpt file ?? production MD for another 200 ns ) repeat 3: same .cpt file ?? production MD for another 200 ns .. Of course, the 3rd way is easier. But does it mean it may not cover enough conformations, as they tend to be more resembled from each other than the 1st approach? Is there a standard way to handle the repeats? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
Thank you Justin and Qinghua! Can I ask 1) I could not find "nstfout" (forces) in the md.mdp file from the tutorial. Should I add a new line of "nstfout=0"? 2) should I change "nstxout-compressed=5000" to "nstxout-compressed=5"? 3) Do you mean using "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>;"gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Subject: Re: How to run MD with longer recording interval to reduce the file size? Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 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>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: 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 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List b
Re: [gmx-users] How to run MD with longer recording interval to reduce the file size?
Dear Qinghua, Thank you very much. Do you mean set "nstvout" and "nstenergy" as 0? Also, how to set xtc-grps as a group? The original md.mdp file is: title = OPLS MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 fs = 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps nstxout-compressed = 5000 ; save compressed coordinates every 10 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 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>; Date: Fri, Dec 15, 2017 06:33 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: 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 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 10 times less file size: i.e. change the following nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 nstxout-compressed = 5000 into nstxout = 5 nstvout = 5 nstenergy = 5 nstlog = 5 nstxout-compressed = 5 Can I ask, if there is something else I need to do in addition to those five "5000"? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How the index is recognised for values more than 99999?
Hi Mark, I only calculate the RMSD for a particular group. So I need to use a index file, which explicitly indicates the atom indices within that group. 1) So if that group indices contain "1 2 3 ...", the Gromacs software will always assume they are 1st, 2nd, 3rd, ... atoms, instead of 11th, 12th, 13th, ... ? 2) And if I want the RMSD for the group containing atom 11th, 12th, 13th, ..., I need to write their indices as 11, 12, 13, ..., ? Thank you. Cheng -- Original -- From: "Mark Abraham";<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 the index is recognised for values more than 9? Hi, The numbering of the coordinate file is not significant for this, precisely for that reason. Mark On Wed, Dec 6, 2017, 7:20 AM ZHANG Cheng <272699...@qq.com> wrote: 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 can the gromacs know it is the 1st atom, instead of the 11th atom? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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 can the gromacs know it is the 1st atom, instead of the 11th atom? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?
Dear Justin and Peter, Thank you so much! I did not realise the meaning of two prompts until now. I was always using the same number for the two prompts. Thank you for the MDAnalysis! https://www.mdanalysis.org/pages/learning_MDAnalysis/ Yours sincerely Cheng -- 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 selected group? Dear Justin, Thank you for confirming this. May I ask, 1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently calculate the RMSD of given residue(s)"? My current command is (by selecting the residue in the "index.ndx" file): gmx rms -s md_0_1.tpr -f 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";<272699...@qq.com>; Date: Fri, Nov 24, 2017 00:20 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: 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, the software will align the selected group to the group in the reference, as much as possible. Then the software calculates the root mean square deviation. As a result, though a protein may deviate a lot from its reference structure, if only one residue is selected for RMSD, the relative positions of the atoms within that residue still remain almost the same relative coordination, which makes their RMSD only 0.01-0.02 nm. Can I ask if my understanding is correct? I wonder, if I can write some script (e.g. python) to manually extract the coordinates information from various frames in the xtc/trr file? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?
Dear Justin, Thank you for confirming this. May I ask, 1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently calculate the RMSD of given residue(s)"? My current command is (by selecting the residue in the "index.ndx" file): gmx rms -s md_0_1.tpr -f 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";<272699...@qq.com>; Date: Fri, Nov 24, 2017 00:20 AM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: 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, the software will align the selected group to the group in the reference, as much as possible. Then the software calculates the root mean square deviation. As a result, though a protein may deviate a lot from its reference structure, if only one residue is selected for RMSD, the relative positions of the atoms within that residue still remain almost the same relative coordination, which makes their RMSD only 0.01-0.02 nm. Can I ask if my understanding is correct? I wonder, if I can write some script (e.g. python) to manually extract the coordinates information from various frames in the xtc/trr file? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[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, the software will align the selected group to the group in the reference, as much as possible. Then the software calculates the root mean square deviation. As a result, though a protein may deviate a lot from its reference structure, if only one residue is selected for RMSD, the relative positions of the atoms within that residue still remain almost the same relative coordination, which makes their RMSD only 0.01-0.02 nm. Can I ask if my understanding is correct? I wonder, if I can write some script (e.g. python) to manually extract the coordinates information from various frames in the xtc/trr file? Thank you. Yours sincerely Cheng -- 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 requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
