[gmx-users] Protein is Jumping from water Box

Dear Gromacs users, I have run 40 ns simulation , after 20 ns simulation my protein is continuously jumping from water Box. Is there any periodic boundary conditions issue with my system or an other error is that . Kindly give your valuable remarks. Thanks, Regards,  Abid Ali Channa, Junior

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

Hi, thank you for your kindly reply... system has been successfully minimized, restrained NVT/NPT equilibrated, and unrestrained Classical MM before... there is no problem.. * here is my equilibrated structure (strarting configuration for qmmm)

Re: [gmx-users] mdrun -rerun does not reproduce itself

On Tue, Apr 26, 2016 at 10:48 PM, Mark Abraham wrote: > Hi, > > Thanks (yet again) for your vigilance! > > On Tue, Apr 26, 2016 at 7:44 PM Christopher Neale < > chris.ne...@alum.utoronto.ca> wrote: > > > Dear Users: > > > > I find that running gromacs 5.1.2 mdrun -rerun

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

Hi, thank you for your kindly reply... system has been successfully minimized, restrained NVT/NPT equilibrated, and unrestrained Classical MM before... there is no problem.. * here is my equilibrated structure (strarting configuration for qmmm)

Re: [gmx-users] mdrun -rerun does not reproduce itself

Dear Mark: Thank you very much for the detailed reply. Everything that you say makes sense. My motivation to investigate this is to predict hamiltonian replica exchange acceptance probabilities in order to develop a good schedule for hamiltonian changes. The energy difference within a given

Re: [gmx-users] mdp options to generate xtc file but not trr file

On 4/26/16 5:11 PM, Metallo Devasto wrote: How can i set mdp option to have a simulation that generate only the xtc file but without the trr file? ( i don't need trr and it has 2 times the size of the xtc file) my mdp option now are nstxout = 1000 nstvout = 1000 Set the above two options

Re: [gmx-users] DSSP with custom residues

On 4/26/16 1:10 PM, leila salimi wrote: Thanks very much. I have one problem, I am trying to use xpm2ps to plot the secondary structure! I used the m2p file from this link: http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) My problem is that the plot is not

[gmx-users] mdp options to generate xtc file but not trr file

How can i set mdp option to have a simulation that generate only the xtc file but without the trr file? ( i don't need trr and it has 2 times the size of the xtc file) my mdp option now are nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstxtcout = 100 nstcalcenergy = -1

Re: [gmx-users] mdrun -rerun does not reproduce itself

Hi, Thanks (yet again) for your vigilance! On Tue, Apr 26, 2016 at 7:44 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear Users: > > I find that running gromacs 5.1.2 mdrun -rerun many times gives different > energies for some components. Indeed. This is the intended

[gmx-users] mdrun -rerun does not reproduce itself

Dear Users: I find that running gromacs 5.1.2 mdrun -rerun many times gives different energies for some components. On GPUs I find that its the SR interactions (both LJ and q) that are inconsistent. On CPU only, I find that its the Coul. recip. that is inconsistent. On CPU only with NPME=1 I

Re: [gmx-users] DSSP with custom residues

Thanks very much. I have one problem, I am trying to use xpm2ps to plot the secondary structure! I used the m2p file from this link: http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2) My problem is that the plot is not correct. I tried different xbox and ybox but it

Re: [gmx-users] Constant Density

Hi Anthony, One possible way I can think of to get the water to redistribute is to perform some temperature annealing of just the solvent, i.e. raise the temperature every so many steps to a max ~500K then quickly quench (lower the temperature) the solvent back to the physiological regime.

Re: [gmx-users] Bash scripting and Gromacs

Or since you have a highly predictable sequence of integers, use a loop over them! Bash built in printf can also be useful here. Stackoverflow.com is a good friend for recipes. Mark On Tue, 26 Apr 2016 17:52 Fabricio Cannini wrote: > On 26-04-2016 10:33, James Starlight

Re: [gmx-users] Bash scripting and Gromacs

On 26-04-2016 10:33, James Starlight wrote: No, in my case it recognize ? like a ? in script I have for sim in ${HOME}/${tit}* ; do if [[ -d $sim ]]; then simulation=$(basename "$sim") cd ${sim} rm dd_dump_err*.pdb trjconv -s md_${tit}?.tpr -f md_${tit}?.trr -o

Re: [gmx-users] DSSP with custom residues

Ok. Thank you very much! //Stephanie Den 26 apr 2016 15:00 skrev "Justin Lemkul" : > > > On 4/26/16 8:57 AM, Stephanie Jephthah wrote: > >> Hi! >> >> I'm simulating a protein conjugate and thus uses custom residues. Is there >> any way to make the dssp program aware of the

[gmx-users] LINCS warning of QMMM simulation

Dear gromacs users i was trying to simulate simple QMMM of 2-chlorobutanol versus protonated water... my simulation was going well until LINCS warning appeared. "Step 34, time 0.017 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.19, max 0.231421 (between atoms 2

Re: [gmx-users] Higher Density than Expected

Hey :) Salt water has a higher density than pure water anyway. Cheers, Tsjerk On Apr 26, 2016 5:19 PM, "Christopher Schlicksup" wrote: > Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the > tip3p water model found approximately this value at 300K,

Re: [gmx-users] Higher Density than Expected

Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the tip3p water model found approximately this value at 300K, and it is also the approximate experimental value. So I guess my question was whether 1025kg/m^3 was off enough to be a concern. I think you answered the question:

Re: [gmx-users] Bash scripting and Gromacs

> On 26 Apr 2016, at 15:33, James Starlight wrote: > > No, in my case it recognize ? like a ? > > in script I have > > for sim in ${HOME}/${tit}* ; do > if [[ -d $sim ]]; then > simulation=$(basename "$sim") > cd ${sim} > rm dd_dump_err*.pdb > trjconv -s

[gmx-users] Constant Density

Hi all, At the risk of bending the rules of thermodynamics, I¹m wondering whether Gromacs can maintain density of a water box (0.750 g/L density of water in a collagen fibril environment) whilst applying an NPT ensemble? gmx_d solvate, fills up to 2/3 of my truncated oct cell, with my protein at

Re: [gmx-users] Bash scripting and Gromacs

No, in my case it recognize ? like a ? in script I have for sim in ${HOME}/${tit}* ; do if [[ -d $sim ]]; then simulation=$(basename "$sim") cd ${sim} rm dd_dump_err*.pdb trjconv -s md_${tit}?.tpr -f md_${tit}?.trr -o ${HOME}/output/${simulation}.xtc -n -pbc mol -ur compact -fit trans

Re: [gmx-users] DSSP with custom residues

On 4/26/16 9:10 AM, leila salimi wrote: Hi Justin, I am also busy by DSSP analysis. I am interested to know what the difference between do_dssp and dssp is? dssp is a binary that actually carries out the DSSP analysis; it is not a GROMACS program but is downloaded from an external source.

Re: [gmx-users] DSSP with custom residues

Hi Justin, I am also busy by DSSP analysis. I am interested to know what the difference between do_dssp and dssp is? Regards, Leila On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul wrote: > > > On 4/26/16 8:57 AM, Stephanie Jephthah wrote: > >> Hi! >> >> I'm simulating a

Re: [gmx-users] DSSP with custom residues

On 4/26/16 8:57 AM, Stephanie Jephthah wrote: Hi! I'm simulating a protein conjugate and thus uses custom residues. Is there any way to make the dssp program aware of the custom residues (and does it make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm assuming that the

[gmx-users] DSSP with custom residues

Hi! I'm simulating a protein conjugate and thus uses custom residues. Is there any way to make the dssp program aware of the custom residues (and does it make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm assuming that the problem is not with do_dssp but with dssp, but please

Re: [gmx-users] Topology include file " " not found

Yeah, don't use wysiwyg word processors for editing plain text files (else you will get such smartness tripping you up). Use an editor aimed at them. Mark On Tue, 26 Apr 2016 13:59 gozde ergin wrote: > Ok I found the error. I put “cis-pinonic.itp” instead of >

Re: [gmx-users] REMD--how to determine the temperature distribution

When I choose NVT, it appear like this: "ERROR: Can not do constant volume yet!”, do you have other ways to determine the temperature except the two websites? > 在 2016年4月26日，下午8:16，Mark Abraham 写道： > > No, just choose NVT. > > Mark > > On Tue, 26 Apr 2016 13:42

Re: [gmx-users] REMD--how to determine the temperature distribution

No, just choose NVT. Mark On Tue, 26 Apr 2016 13:42 YanhuaOuyang <15901283...@163.com> wrote: > Thank you so much, but the latter one is only suitable for REMD in NPT > ensemble. > > 在 2016年4月26日，上午1:20，Christopher Neale 写道： > > > > There are many published

Re: [gmx-users] g_hbond: range checking error

Hi, Strange. Do you get the same error with 5.1.2? If so, can you please file a redmine issue (http://redmine.gromacs.org/) and upload the input files that generate this error? Assign the issue to me. Kind regards Erik Marklund On 26 Apr 2016, at 12:01, Shubhangi Gupta

Re: [gmx-users] Topology include file " " not found

Ok I found the error. I put “cis-pinonic.itp” instead of ”cis-pinonic.itp”. The problem is quote. On 26 Apr 2016, at 13:35, gozde ergin wrote: > > I checked it and there is no #include statement in cis-pinonic.itp file. >> On 26 Apr 2016, at 13:24, Justin Lemkul

Re: [gmx-users] Free energy including change in temperature

On 4/26/16 7:48 AM, Andreas Mecklenfeld wrote: Dear Gromacs users, I would like to try a free energy calculation including a change in temperature using the temperature-lambdas-vector. It says in the online manual that each entry has to be between 0 and 1. How can I define the corresponding

[gmx-users] Free energy including change in temperature

Dear Gromacs users, I would like to try a free energy calculation including a change in temperature using the temperature-lambdas-vector. It says in the online manual that each entry has to be between 0 and 1. How can I define the corresponding temperatures (something like couple-lambda0 /

Re: [gmx-users] REMD--how to determine the temperature distribution

Thank you so much, but the latter one is only suitable for REMD in NPT ensemble. > 在 2016年4月26日，上午1:20，Christopher Neale 写道： > > There are many published approaches. Here is the one that I use: > http://origami.phys.rpi.edu/racc/rate_of_acceptance.php > Another

Re: [gmx-users] Topology include file " " not found

I checked it and there is no #include statement in cis-pinonic.itp file. > On 26 Apr 2016, at 13:24, Justin Lemkul wrote: > > > > On 4/26/16 5:57 AM, gozde ergin wrote: >> Dear all, >> >> I am trying to simulate organic system. >> Here is my tool.top file, and cis-pionic,its

Re: [gmx-users] Topology include file " " not found

On 4/26/16 5:57 AM, gozde ergin wrote: Dear all, I am trying to simulate organic system. Here is my tool.top file, and cis-pionic,its is in the same folder with the tool.top. ; ; Topology from .mol2 file ; topolbuild ; ; The force field files to be included #include

[gmx-users] g_hbond: range checking error

Hi all, I want to calculate the number of hydrogen bonds between protein and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups - protein and SOL. When i run the command, I get a *Range Checking error* *Variable gx has value -3. It should have been within [0 ..19]*

Re: [gmx-users] Bash scripting and Gromacs

> On 26 Apr 2016, at 11:22, James Starlight wrote: > > Exactly the problem was there! > > BTW how to define selection more carefully (avoiding using *) tpr and > trr to be sure that always only 1 file is selected assuming that all > relevant trajectories and topologies

[gmx-users] Topology include file " " not found

Dear all, I am trying to simulate organic system. Here is my tool.top file, and cis-pionic,its is in the same folder with the tool.top. ; ; Topology from .mol2 file ; topolbuild ; ; The force field files to be included #include "charmm27.ff/forcefield.itp" ; Include chain topologies #include

Re: [gmx-users] Adding Residue in .rtp file.

On 4/26/16 2:57 AM, Md. Imrul Reza Shishir wrote: Dear All ​I have a ​structure file(pdb) cellulose fibril with unknown residue and atom type. I want to add this residue in the .rtp file and .hdb file. As i am new in gromacs. Is there any tutorial how i parameterize the structure file with

Re: [gmx-users] Bash scripting and Gromacs

Exactly the problem was there! BTW how to define selection more carefully (avoiding using *) tpr and trr to be sure that always only 1 file is selected assuming that all relevant trajectories and topologies are differs only on the digit e.g resp_complex_conf7/md_resp_complex_conf7.tpr

Re: [gmx-users] Bash scripting and Gromacs

> On 26 Apr 2016, at 11:00, James Starlight wrote: > > Hello, > > I faced with the folliwing problem: > > I try to make small script which will loop several folders > corresponded to the invididual simulations and procecc each trajectory > searching them by the keyword

[gmx-users] Bash scripting and Gromacs

Hello, I faced with the folliwing problem: I try to make small script which will loop several folders corresponded to the invididual simulations and procecc each trajectory searching them by the keyword trr_file="md_resp_complex_conf" #!/bin/bash

Re: [gmx-users] Syntax error

Sorry, I found my mistake. Should have read the instructions properly. My bad  On 4/26/16, Roshan Shrestha wrote: > I am currently working on KALP-15 tutorial. After I typed- > > gmx editconf -f protein.gro -o protein_newbox.gro -box (membrane box > vectors) -center x y z >

Re: [gmx-users] Standard volume of the simulation box

Hi Sana, There's no such thing as a standard volume. The key decision you have to take is what distance there should be between periodic images, for which the consensus view is that you need at least 2.0 nm. I typically use 2.25, corresponding roughly to 9 layers of water, so the protein can

Re: [gmx-users] Syntax error

You have to provide the actual box vectors value in numbers eg: -box 9 5 6 regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai Mumbai, 400-076, India On 26 April 2016 at

[gmx-users] Syntax error

I am currently working on KALP-15 tutorial. After I typed- gmx editconf -f protein.gro -o protein_newbox.gro -box (membrane box vectors) -center x y z I got bash: syntax error near unexpected token `(' What is the remedy to this problem ? -- Gromacs Users mailing list * Please search the

[gmx-users] Adding Residue in .rtp file.

Dear All ​I have a ​structure file(pdb) cellulose fibril with unknown residue and atom type. I want to add this residue in the .rtp file and .hdb file. As i am new in gromacs. Is there any tutorial how i parameterize the structure file with force field. Is there any tutorial or guideline how to

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

Yes On Tue, 26 Apr 2016 08:12 Husen R wrote: > Hi, > > > Thanks for your reply. > > There is no state.cpt or state_prev.cpt file. > > In equilibration part 1 the resulting checkpoint files : nvt.cpt and > nvt_prev.cpt > In equilibration part 2 the resulting checkpoint files :

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

Hi, Thanks for your reply. There is no state.cpt or state_prev.cpt file. In equilibration part 1 the resulting checkpoint files : nvt.cpt and nvt_prev.cpt In equilibration part 2 the resulting checkpoint files : npt.cpt and npt_prev.cpt In Production MD the resulting checkpoint files :