[gmx-users] RE: RE: Doubts over g_lie usage

Thanks for that explanation. I would like to know this with little more detail. What do you mean by RF-0 and which cut-off value are you talking about? Rerunning the trajectory means the whole MD run again? Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-ove

[gmx-users] RE: RE: Doubts over g_lie usage

PME has a reciprocal component of the energy that cannot be calculated for each individual atom. Hence it can't be assigned to an energy group (at least that is my understanding). I just use RF-0 to rerun the trajectory using a much larger cut off to try and account for the errors that way. At l

Re: [gmx-users] desired no of water molecules

sorry '-maxsol' On Tue, Aug 14, 2012 at 11:24 AM, tarak karmakar wrote: > Oh !! > I got it it is not the -nmol but '-maxmol' > thanks to both of u...:) > > On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai wrote: >> hmm. What happens if you try -maxsol instead of -nmol? >> >> On 2012-08-14

Re: [gmx-users] desired no of water molecules

Oh !! I got it it is not the -nmol but '-maxmol' thanks to both of u...:) On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai wrote: > hmm. What happens if you try -maxsol instead of -nmol? > > On 2012-08-14 10:24:18AM +0530, tarak karmakar wrote: >> This is the ala.gro (alanine dipeptide) fi

[gmx-users] RE: Doubts over g_lie usage

Dear Tom, The explanation really helps me understand LIE much more clearer. What's the issue if I have used PME coulombtype? I have actually used PME. Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-over-g-lie-usage-tp5000130p5000146.html Sent fr

Re: [gmx-users] Parrinello-Rahman with surface-tension coupling

On 13/08/2012 7:21 PM, Felipe Pineda, PhD wrote: Dear All, the Gromacs User Manual V.4.5.4 states on p. 33: "(...) the surface tension and the z-component of the pressure can be coupled to a pressure bath. Presently, this only works with the Berendsen pressure coupling algorithm in GROMACS."

Re: [gmx-users] Questions regarding Polarization Energy Calculation

On 14/08/2012 7:38 AM, jesmin jahan wrote: Dear Gromacs Users, I have some questions regarding GB-Polarization Energy Calculation with Gromacs. I will be grateful if someone can help me with the answers. I am trying to calculate GB-Polarization energy for different Protein molecules. I am inter

[gmx-users] RE: Doubts over g_lie usage

You need to assign your own experimentally determined values to -Elj and -Eqq. These are determined by simulating your ligand in a solvent box. g_lie uses some common values found in the literature for -Clj and -Cqq again you need to decide if they are appropriate in your case. Try reading papers

Re: [gmx-users] desired no of water molecules

hmm. What happens if you try -maxsol instead of -nmol? On 2012-08-14 10:24:18AM +0530, tarak karmakar wrote: > This is the ala.gro (alanine dipeptide) file which does not contain > any water (SOL) a priori. > > Grunge ROck MAChoS >22 > 1ACE HH311 1.267 1.058 1.673 > 1ACE

Re: [gmx-users] desired no of water molecules

On 14/08/2012 2:37 PM, tarak karmakar wrote: Thanks for the quick reply, I have given this command to add 612 water molecules. genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top That's not how to use -nmol, nor is it the right option to solve your problem. There's an option

Re: [gmx-users] desired no of water molecules

This is the ala.gro (alanine dipeptide) file which does not contain any water (SOL) a priori. Grunge ROck MAChoS 22 1ACE HH311 1.267 1.058 1.673 1ACECH32 1.364 1.086 1.631 1ACE HH323 1.422 0.996 1.607 1ACE HH334 1.416 1.148 1.70

Re: [gmx-users] implicit solvent protein simulations with charmm

On 14/08/2012 1:07 AM, Sai Pooja wrote: Hi, I have read a couple of posts on related topics but I am still not sure how to proceed and would be grateful to get some help. I want to run implicit solvent simulations of a protein+water (implicit) system in the canonical ensemble using charmm27+cma

Re: [gmx-users] desired no of water molecules

Did you have waters in the system before adding another 612? I don't know how VMD counts waters, but another way is to grep -c for SOL in the resulting gro file and divide by 3. On 2012-08-14 10:07:54AM +0530, tarak karmakar wrote: > Thanks for the quick reply, I have given this command to add 6

Re: [gmx-users] desired no of water molecules

Thanks for the quick reply, I have given this command to add 612 water molecules. genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top But in the solvated file, I see there are 668 water molecules. A part of the output while adding water molecules is as follows Using plugin gro

Re: [gmx-users] trajectory file formats

On 14/08/2012 2:23 AM, Broadbent, Richard wrote: As these are binary files the formatting can be quite complex I would suggest using the library available here: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library This includes all the functions necessary to read/write these form

Re: [gmx-users] potential energy

On 14/08/2012 11:07 AM, Tom Dupree wrote: Greetings all, Can I easily obtain the potential energy for a energy group rather than the whole simulation cell? Yes. See manual 3.3 and 7.3.8. But below you imply you're already doing this. You can make custom groups - see http://www.gromacs.org/D

Re: [gmx-users] desired no of water molecules

On 14/08/2012 2:02 PM, tarak karmakar wrote: Dear All, Is there any way to add a specific number of water ( let say 650 water) molecules while dissolving the solute in a given box ? Check out genbox -h Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

Re: [gmx-users] checkpoint file

On 14/08/2012 6:08 AM, Juliette N. wrote: Yes this is to continue a crashed run, but I dont know why my runs crash at the very beginnig of the simulation. You have to look at the stderr, stdout and .log file for information. You can't solve the problem without that. Mark I am using 4.5.4

Re: [gmx-users] a residue move in extremely large scale in MD

On 14/08/2012 7:53 AM, Dallas Warren wrote: >From your comments, it appears that you have not watched the trajectory for you system. This is really something that everyone should do with the systems they are simulating, as you can gain a lot of information from looking visually at it. Lookin

[gmx-users] desired no of water molecules

Dear All, Is there any way to add a specific number of water ( let say 650 water) molecules while dissolving the solute in a given box ? Thanks, Tarak -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! *

[gmx-users] Doubts over g_lie usage

Hello everyone, I have a doubt about LIE calculation using g_lie in gromacs. This doubt is about the values automatically assigned for -Clj and -Cqq flags when I ran the following command: $ g_lie -f J32_md10ns.edr -o LIE_1A1_J32.xvg -b 7001 -e 1 -ligand J32 The following text contains my op

[gmx-users] potential energy

Greetings all, Can I easily obtain the potential energy for a energy group rather than the whole simulation cell? Does it make any sense to do so? I am simulating protein ligand complexes and have observed movement in some cases. When I analyse the interaction energy sum of LJ and columbic of LI

Re: [gmx-users] checkpoint file

On 8/13/12 5:10 PM, Juliette N. wrote: All right, but I was expecting some more information reflecting the last state of the system, e.g, velocities... gmxcheck verifies the integrity of the file. gmxdump will produce more detailed information, not that it's of any particular use in this c

RE: [gmx-users] a residue move in extremely large scale in MD

>From your comments, it appears that you have not watched the trajectory for >you system. This is really something that everyone should do with the systems >they are simulating, as you can gain a lot of information from looking >visually at it. Looking at 0.5ns snap shots is not watching the t

[gmx-users] Questions regarding Polarization Energy Calculation

Dear Gromacs Users, I have some questions regarding GB-Polarization Energy Calculation with Gromacs. I will be grateful if someone can help me with the answers. I am trying to calculate GB-Polarization energy for different Protein molecules. I am interested both in energy values with the time req

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

Oh something I didn't mention: for bond constraints I used h-bonds instead of all-bonds. This may or may not make a difference (although I switched to h-bonds based on the suggestion of some charmm/lipid thread on here from a couple of years ago). On 2012-08-09 12:34:19PM -0300, Sebastien Cote wro

Re: [gmx-users] checkpoint file

All right, but I was expecting some more information reflecting the last state of the system, e.g, velocities... Thank you, On 13 August 2012 17:04, Justin Lemkul wrote: > > > On 8/13/12 4:54 PM, Juliette N. wrote: >> >> Hi all, >> >> My cpt file doesnt contain any information?!! >> > > Sure i

Re: [gmx-users] checkpoint file

On 8/13/12 4:54 PM, Juliette N. wrote: Hi all, My cpt file doesnt contain any information?!! Sure it does. gmxcheck -f md.cpt gives the following: Checking file md.cpt # Atoms 20688 Last frame -1 time 7468.965 Item#frames Timestep (ps) Step 1 T

Re: [gmx-users] checkpoint file

Hi all, My cpt file doesnt contain any information?!! gmxcheck -f md.cpt gives the following: Checking file md.cpt # Atoms 20688 Last frame -1 time 7468.965 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Veloci

Re: [gmx-users] checkpoint file

Thanks, maybe I should re start ... :( On 13 August 2012 16:36, Justin Lemkul wrote: > > > On 8/13/12 4:34 PM, Juliette N. wrote: >> >> I am using the same line, but it crashes...Is that because my trr >> files is big that it cand append the files? It was ~ 40 GB when crash >> happened... >> >>

Re: [gmx-users] checkpoint file

On 8/13/12 4:34 PM, Juliette N. wrote: I am using the same line, but it crashes...Is that because my trr files is big that it cand append the files? It was ~ 40 GB when crash happened... I am using 4.5.4. I tried both with and without -append. If it fails with and without the -append option

Re: [gmx-users] checkpoint file

I am using the same line, but it crashes...Is that because my trr files is big that it cand append the files? It was ~ 40 GB when crash happened... I am using 4.5.4. I tried both with and without -append. On 13 August 2012 16:19, Justin Lemkul wrote: > > > On 8/13/12 4:16 PM, Juliette N. wrote

Re: [gmx-users] checkpoint file

On 8/13/12 4:16 PM, Juliette N. wrote: Sorry Justin, but I dont see whats happening... Do I have to remove mpi or -np from the line while using -cpi *.cpt ? No, you don't. All you should need (provided the .cpt file is valid, which it appears to be from the gmxcheck output from before) is:

Re: [gmx-users] checkpoint file

Sorry Justin, but I dont see whats happening... Do I have to remove mpi or -np from the line while using -cpi *.cpt ? mdrun -deffnm md -s -o -c -g -e -x -cpi >& output Thanks! On 13 August 2012 16:10, Justin Lemkul wrote: > > > On 8/13/12 4:08 PM, Juliette N. wrote: >> >> Yes this is to conti

Re: [gmx-users] checkpoint file

On 8/13/12 4:08 PM, Juliette N. wrote: Yes this is to continue a crashed run, but I dont know why my runs crash at the very beginnig of the simulation. I am using 4.5.4 so -append should work by default. I tried a simulation from time zero and it works as before ( mpirun -np 8 mdrun_mpi -deff

Re: [gmx-users] checkpoint file

Yes this is to continue a crashed run, but I dont know why my runs crash at the very beginnig of the simulation. I am using 4.5.4 so -append should work by default. I tried a simulation from time zero and it works as before ( mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x ) but as soon as I

Re: [gmx-users] grommp warning

On 8/13/12 3:47 PM, Shima Arasteh wrote: OK, thanks. But please let me know something: Is the "pressure coupling with absolute position restraints" is an option to fix a volume significantly? If yes, then It's me to think about keeping fix the volume of my system or not. You can't have con

Re: [gmx-users] checkpoint file

Am 13.08.2012 21:42, schrieb Juliette N.: Thank you. I am using mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt I see a "md_prev.cpt". If I presume correctly that this is for the continuation of the crashed run: Why and did you read what I wrote? but I dont get any

Re: [gmx-users] Topology file for simulation of inorganic compounds

On 2012-08-13 21:39, Justin Lemkul wrote: On 8/13/12 1:49 PM, Deepak Ojha wrote: Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the sam

Re: [gmx-users] grommp warning

OK, thanks. But please let me know something: Is the "pressure coupling with absolute position restraints" is an option to fix a volume significantly? If yes, then It's me to think about  keeping fix the volume of my system or not. Thanks, believe me I got this point through the mailing list :-)

Re: [gmx-users] checkpoint file

On 8/13/12 3:42 PM, Juliette N. wrote: Thank you. I am using mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt but I dont get any output and the issued command terminates in the terminal. Normally error messages are rather obvious. Check your .log file carefully or

Re: [gmx-users] checkpoint file

Thank you. I am using mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x -cpi md_prev.cpt but I dont get any output and the issued command terminates in the terminal. Do I have to remove the -o -c -g -e -x flags from the command line? Appreciate your help, On 13 August 2012 15:28, Matthias

Re: [gmx-users] Topology file for simulation of inorganic compounds

On 8/13/12 1:49 PM, Deepak Ojha wrote: Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the same. Likely you will have to do it manuall

Re: [gmx-users] grommp warning

On 8/13/12 12:36 PM, Shima Arasteh wrote: Dear gmx users, I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings. Anybody knows about this warning? Yes, and there are several posts in the list archive explaining its origin, interpreta

Re: [gmx-users] checkpoint file

Long story short: backup everything (since it's a backup, and hopefully you won't need it), then use the [whatever].cpt file. You don't want to do work twice, do you? If you use the [whatever]_prev.cpi file, you will calculate some frames *again* that are already there. If you use an up-to-date

[gmx-users] checkpoint file

Hello all, I am going to restart my crashed simulations, but I am not sure which of *_prev.cpt or *.cpt to use as they contain different written frames. *_prev.cpt Last frame -1 time 7462.900 *.cpt Last frame -1 time 7468.965 Also on the gmx site it is sta

[gmx-users] grommp warning

Dear gmx users, I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings. Anybody knows about this warning? The warning is : WARNING 1 [file NPT.mdp]:   You are using pressure coupling with absolute position restraints, this   will give ar

[gmx-users] Topology file for simulation of inorganic compounds

Dear All I want to do simulation of some ions like azide ion,thiocynate ion and other inorganic compounds in liquid water. I am not sure how to generate topology file for the same.How can I go about doing the same. -- DeepaK Ojha School Of Chemistry "Selfishness is not living as one wishes to li

[gmx-users] grommp warning

Dear gmx users, I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings. Anybody knows about this warning? The warning is : WARNING 1 [file NPT.mdp]:   You are using pressure coupling with absolute position restraints, this   will give arti

Re: [gmx-users] trajectory file formats

As these are binary files the formatting can be quite complex I would suggest using the library available here: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library This includes all the functions necessary to read/write these formats and is licensed under LGPL. Richard On 13/08

[gmx-users] implicit solvent protein simulations with charmm

Hi, I have read a couple of posts on related topics but I am still not sure how to proceed and would be grateful to get some help. I want to run implicit solvent simulations of a protein+water (implicit) system in the canonical ensemble using charmm27+cmap forcefield. I am trying to use the param

[gmx-users] trajectory file formats

I have written a unique MD program and want to output a full-precision trajectory containing coordinate, velocity, and force information in a .trr or a .trj formatted file.  Where in the gromacs code can I find a description of the formats of these files and an example of how they are written? A

Re: [gmx-users] time evolutions of an angle

On 13/08/2012 10:11 PM, akn wrote: Dear gmx users, How can I calculate the time evolutions of an angle in the molecules in the system? Various ways. Check out manual section 7.4 for clues, and chapter 8 and appendix D for more details. Mark -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: mass center of each molecule

On 13/08/2012 10:03 PM, akn wrote: Dear Justin, Thank you very much for your answer. I specified each molecule individually in index file and I used trjconv -sep command to seperate the system each step (conf1.gro, conf2.gro, conf3.gro, conf4.gro). Then I used script that you suggested, it was

[gmx-users] time evolutions of an angle

Dear gmx users, How can I calculate the time evolutions of an angle in the molecules in the system? Thanks, Akn. -- View this message in context: http://gromacs.5086.n6.nabble.com/time-evolutions-of-an-angle-tp595.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com

[gmx-users] Re: mass center of each molecule

Dear Justin, Thank you very much for your answer. I specified each molecule individually in index file and I used trjconv -sep command to seperate the system each step (conf1.gro, conf2.gro, conf3.gro, conf4.gro). Then I used script that you suggested, it was as; groups=`grep "^\[" index.ndx

[gmx-users] Parrinello-Rahman with surface-tension coupling

Dear All, the Gromacs User Manual V.4.5.4 states on p. 33: "(...) the surface tension and the z-component of the pressure can be coupled to a pressure bath. Presently, this only works with the Berendsen pressure coupling algorithm in GROMACS." My question: does this hold for V. 4.5.5 as well