Re: RE: [gmx-users] find the relevant structure out

- Original Message - From: #ZHAO LINA# Date: Wednesday, November 24, 2010 17:52 Subject: RE: [gmx-users] find the relevant structure out To: Discussion list for GROMACS users > Hi, > > Thanks for your answering. > > Due to the difference in assignment, so I wonder which one I > sho

RE: [gmx-users] find the relevant structure out

Hi, Thanks for your answering. Due to the difference in assignment, so I wonder which one I should build a bit much more faith on? I read (by eyes) the ss.xpm produced by do_dssp, and find the relevant resi out which showed as beta-sheet, but in pymol, it's really so standard alpha-helix, w

[gmx-users] LINCS Warnings in the middle of an MD run

Dear All, About the Lincs warnings in Christoph Meier’ problem, is there any improved method or a better way to deal with them? What we can do is to use shorter timesteps or re-start the simulation using a frame before the first lincs warning? [gmx-users] LINCS Warnings in the middle of an MD

Re: [gmx-users] mdrun crashed with tables

Hi all, 1) added -table tablefile1 -table tablefile2 etc.. to mdrun command ... 2)Increased table-extension parameter from 0.0 to 1.0 and added those values to the table too... Works now! Thanks Mark and ms! Pooja On Tue, Nov 23, 2010 at 7:03 PM, Mark Abraham wrote: > On 24/11/2010 8:42 AM,

Re: [gmx-users] find the relevant structure out

Hi, > Visualization software can sometimes assign the secondary structure > incorrectly. There has been an interesting discussion on this on the Pymol user list years ago (http://www.mail-archive.com/pymol-us...@lists.sourceforge.net/msg01574.html). Secondary structure assignment is foremost hu

Re: [gmx-users] error found in gmx

On 24/11/2010 3:09 PM, ITHAYARAJA wrote: Hi Dear, I found a fatal error as I running pdb2gmx command, Which shows that incomplete ring in HIS341. I am very confused what it's meant and how do i solve the problem? Please any body give me a reasonable solution for that You need to be providi

Re: [gmx-users] error found in gmx

Hi Ithayaraja, That's not an error in pdb2gmx. It's an error in your input file. One of your residues (H341) is not complete. This is the first thing to check when going for a simulation. You'll have model the missing atoms in before you can proceed. Cheers, Tsjerk On Wed, Nov 24, 2010 at 5:09

[gmx-users] error found in gmx

Hi Dear, I found a fatal error as I running pdb2gmx command, Which shows that incomplete ring in HIS341. I am very confused what it's meant and how do i solve the problem? Please any body give me a reasonable solution for that thank you -- -- *With love and gratitude of,* Ithayaraja M, Resea

[gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU

Hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors d

[gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU

hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors dete

Re: [gmx-users] mdrun crashed with tables

On 24/11/2010 8:42 AM, Sai Pooja wrote: Hi, I run a simulation of a protein in water(tip3p) system using charmm forcefield. I have specified the following energy groups: Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype to User and VdW to Cut-off. I then generate tables

Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

On 24/11/2010 5:04 AM, ms wrote: On 23/11/10 17:00, Mark Abraham wrote: There is no general solution for bonds visualized on a single set of coordinates, however - over a trajectory, either molecules appear to diffuse out of the box, or appear to break. Yep, but if they appear broken because t

Re: [gmx-users] Run input file prepared by different gmx version

On 24/11/2010 7:17 AM, Deniz KARASU wrote: Hi, I prepared a run input file (tpr file) with gromacs 4.07 and can run this tpr on a 4.5.3 installed system. I wonder that there will be a problem about using input files prepared by different gromacs version? Thanks deniz. Generally, no prob

Re: [gmx-users] mdrun crashed with tables

On 23/11/10 21:42, Sai Pooja wrote: Hi, I run a simulation of a protein in water(tip3p) system using charmm forcefield. I have specified the following energy groups: Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype to User and VdW to Cut-off. I then generate tables as s

Re: [gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?

On 24/11/2010 2:22 AM, maria goranovic wrote: I have a trajectory containing around 30,000 frames at 20 ps intervals. When I try to read and analyze this trajectory, most gmx tools can read only one frame. I do not know which one. What did your .mdp file specify for writing? If you wrote (say)

Re: [gmx-users] Residue Residue Contact

nahren manuel skrev 2010-11-23 21.19: Dear Gromacs Users, I was wondering if there is a way in Gromacs to calculate the number of atoms involved in residue-residue contacts (within a given cut-off distance, say 5 A) over the entire trajectory. so if I have 100 residues and 500 frames, I would

RE: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

Using dynamic bonds and vdw representations is also an option. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 -

[gmx-users] mdrun crashed with tables

Hi, I run a simulation of a protein in water(tip3p) system using charmm forcefield. I have specified the following energy groups: Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype to User and VdW to Cut-off. I then generate tables as specified in the manual. To test the va

Re: [gmx-users] Adding custom residue to Charmm FF in Gromacs

Quoting César Ávila : > Hi, > I would like to add topology and parameter information for a custom residue > to the CHARMM forcefield on GROMACS 4.5.3. Which are the files that I should > edit for this? Should I also perform some units conversion? The .rtp and perhaps .hdb (if you need hydrogen re

[gmx-users] Residue Residue Contact

Dear Gromacs Users, I was wondering if there is a way in Gromacs to calculate the number of atoms involved in residue-residue contacts (within a given cut-off distance, say 5 A) over the entire trajectory. so if I have 100 residues and 500 frames, I would end with a 100X100X500 array (where 100

[gmx-users] Run input file prepared by different gmx version

Hi, I prepared a run input file (tpr file) with gromacs 4.07 and can run this tpr on a 4.5.3 installed system. I wonder that there will be a problem about using input files prepared by different gromacs version? Thanks deniz. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] perl script for g_hbond

Quoting leila karami : > Dear Justin > > thank you very much. > > what I used as HB.pl exactly is as follows: > > is there problem in that? > > #!/usr/bin/perl > # > # plot_hbmap.pl - plot the probability of finding a particular hydrogen bond > # based on several input files: > # 1. coordinate f

[gmx-users] perl script for g_hbond

Dear Justin thank you very much. what I used as HB.pl exactly is as follows: is there problem in that? #!/usr/bin/perl # # plot_hbmap.pl - plot the probability of finding a particular hydrogen bond # based on several input files: # 1. coordinate file (for atom naming) - MUST be a .pdb file wi

Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

On 23/11/10 17:00, Mark Abraham wrote: If you only want a snapshot, then simply write a single chosen frame to a .gro or .pdb using trjconv. Load only that into VMD, and it won't generate PBC-crossing bonds. If you want a movie, then there I seem to recall that there is a VMD option to generate

[gmx-users] Adding custom residue to Charmm FF in Gromacs

Hi, I would like to add topology and parameter information for a custom residue to the CHARMM forcefield on GROMACS 4.5.3. Which are the files that I should edit for this? Should I also perform some units conversion? Thanks Cesar -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

Re: [gmx-users] perl script for g_hbond

Quoting leila karami : > Dear Justin > > when I use perl HB.pl -s .pdb -map .xpm -index .ndx, I encountered with: > > syntax error at ./HB.pl line 10, near "nothing else" > "use" not allowed in expression at ./HB.pl line 13, at end of line > Execution of ./HB.pl aborted due to compilation errors.

Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

On 23/11/10 17:00, Mark Abraham wrote: If you want a movie, then there I seem to recall that there is a VMD option to generate bonds for each frame, and not to use those from the first frame. Ask their mailing list. Such bonds will not traverse the PBC, obviously. Just for the record: It seems

[gmx-users] perl script for g_hbond

Dear Justin when I use perl HB.pl -s .pdb -map .xpm -index .ndx, I encountered with: syntax error at ./HB.pl line 10, near "nothing else" "use" not allowed in expression at ./HB.pl line 13, at end of line Execution of ./HB.pl aborted due to compilation errors. -- Leila Karami Ph.D. student of

Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

On 23/11/10 17:00, Mark Abraham wrote: If you only want a snapshot, then simply write a single chosen frame to a .gro or .pdb using trjconv. Load only that into VMD, and it won't generate PBC-crossing bonds. If you want a movie, then there I seem to recall that there is a VMD option to generate

[gmx-users] Re: gmx-users Digest, Vol 79, Issue 152

On Tue, Nov 23, 2010 at 9:55 AM, wrote: > J. Nathan Scott skrev 2010-11-23 17.35: >> Hello Gromacs users, >> >> I was wondering, have the AMBER 11 and/or AMOEBA force fields been >> implemented by anyone for use in Gromacs? The reason I ask is that we >> are very interested in trying some of our

Re: [gmx-users] perl script for g_hbond

Quoting leila karami : > Dear Justin > > thanks for your time and attention > > yes of cource, I copy and paste correctly entire script from (first line) # > ! /usr/bin/perl to (last line) exit. what is your mean of [There should be > more information in the output if the program fails]? which out

[gmx-users] perl script for g_hbond

Dear Justin thanks for your time and attention yes of cource, I copy and paste correctly entire script from (first line) # ! /usr/bin/perl to (last line) exit. what is your mean of [There should be more information in the output if the program fails]? which output? -- gmx-users mailing listg

Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

On 24/11/2010 2:48 AM, ms wrote: Dear GROMACS users, I am trying to visualize a trajectory with hundreds of peptides which come and go out and in the faces of the periodic box. Problem is, when they cross the periodic boundary, the visualization software (I tried both VMD and PyMol) create vi

RE: [gmx-users] find the relevant structure out

Quoting #ZHAO LINA# : > I really do not know how to get those beta-sheet structures out, > or maybe by which ways? > Visualization software can sometimes assign the secondary structure incorrectly. If you have some justifiable reason to believe that a certain secondary structure exists (i.e. DSS

Re: [gmx-users] water model purpose?

On 23/11/2010 8:35 PM, ahmet yıldırım wrote: Hi, pdb2gmx -f 1LYD.pdb -water tip3p Why is -water tip3p command ( tip3p water model) used? What the purpose? This chooses the water model embedded in the system topology written by pdb2gmx. Afterwards, genbox command is already added to solvent

[gmx-users] Re: Please help me solve this fatal error

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the message there and would ask that any future correspondence be conducted there. You're providing an energy file while changing your thermostat. grompp expects that all energy terms wi

Re: [gmx-users] perl script for g_hbond

Quoting leila karami : > Dear Justin > > I study simulation of pr-dna complex. I want to know the percentage of > existence of each hbond during my trajectory. > I searched in previous lists. I want to use Perl script you offered to carla > jamous: > http://lists.gromacs.org/pipermail/gmx-users/20

Re: [gmx-users] AMOEBA/AMBER 11 in Gromacs?

J. Nathan Scott skrev 2010-11-23 17.35: Hello Gromacs users, I was wondering, have the AMBER 11 and/or AMOEBA force fields been implemented by anyone for use in Gromacs? The reason I ask is that we are very interested in trying some of our simulations using the AMOEBA force field but would like

[gmx-users] AMOEBA/AMBER 11 in Gromacs?

Hello Gromacs users, I was wondering, have the AMBER 11 and/or AMOEBA force fields been implemented by anyone for use in Gromacs? The reason I ask is that we are very interested in trying some of our simulations using the AMOEBA force field but would like to stick with the Gromacs engine if at all

Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11/23/2010 04:48 PM, ms wrote: > Dear GROMACS users, > > I am trying to visualize a trajectory with hundreds of peptides which > come and go out and in the faces of the periodic box. Problem is, when > they cross the periodic boundary, the visualiz

Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

Ok, I can update this situation (see below quote): On 18/10/10 03:30, Mark Abraham wrote: And then, I read on the Gromacs website *this* http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints " 2. The manual is a bit unclear about whether this type of dihedral restraint is stable for u

[gmx-users] perl script for g_hbond

Dear Carla thanks for your attention I used : perl HB.pl -s .pdb -map .xpm -index .ndx, but problem is there yet. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

Dear GROMACS users, I am trying to visualize a trajectory with hundreds of peptides which come and go out and in the faces of the periodic box. Problem is, when they cross the periodic boundary, the visualization software (I tried both VMD and PyMol) create visual artefacts by visualizing nons

Re: [gmx-users] perl script for g_hbond

Hi, you should probably do: perl HB.pl -s .pdb -map .xpm -index .xpm More details are written inside the perl script. Cheers, Carla On Tue, Nov 23, 2010 at 4:32 PM, leila karami wrote: > Dear Justin > > I study simulation of pr-dna complex. I want to know the percentage of > existence of each

[gmx-users] perl script for g_hbond

Dear Justin I study simulation of pr-dna complex. I want to know the percentage of existence of each hbond during my trajectory. I searched in previous lists. I want to use Perl script you offered to carla jamous: http://lists.gromacs.org/pipermail/gmx-users/2010-October/054727.html I'm biginner

[gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?

I have a trajectory containing around 30,000 frames at 20 ps intervals. When I try to read and analyze this trajectory, most gmx tools can read only one frame. I do not know which one. For example, g_density will read the entire trajectory, but will finally report that : read 1 frame from traject

Re: [gmx-users] Problem regarding Gromacs - GPU

Hi, The benchmarks are infinite runs (nsteps=-1). Try adding the -maxh option to mdrun to limit the execution time. Rossen On 11/23/10 9:48 AM, kapil mathur wrote: Dear All, I have some queries regarding the benchmarking result of mdrun-gpu : 1. I have run mdrun-gpu with dhfr-impl-1nm.ben

Re: [gmx-users] .itp for simple atom

On 23/11/10 09:43, leila separdar wrote: I am beginner with gromacs I want to simulate a system of 100 Argon atom with Lennard Jones force field but I do not know how to make .itp file I have made this lines but it made error. could anybody hep me? Telling what errors come out would help. [

Re: [gmx-users] Problem regarding Gromacs - GPU

Hi, If you take a look at the mdp file, it becomes obvious that the simulation length is infinite: nsteps = -1 This is useful for a benchmarking setup where you want to run e.g. ~10min case in which you'r use the "-maxh 0.167" mdrun option. Cheers, -- Szilárd On Tue, Nov 23, 201

[gmx-users] .itp for simple atom

I am beginner with gromacs I want to simulate a system of 100 Argon atom with Lennard Jones force field but I do not know how to make .itp file I have made this lines but it made error. could anybody hep me? [ atomtypes ] ;name at.num mass charge ptypesigmaepsilon AR

Re: [gmx-users] deprotonation and DNA

luo jinghui skrev 2010-11-23 10.31: Hi, I am running DNA simulation with amber force field. I did deprotonation on some of adenine group and then add some ions to get system without charge. Do you think this system will be suitable for MD simulation? regards, Jinghui Yes, maybe. It de

[gmx-users] water model purpose?

Hi, pdb2gmx -f 1LYD.pdb -water tip3p Why is -water tip3p command ( tip3p water model) used? What the purpose? Afterwards, genbox command is already added to solvent water as the following: genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro Thanks -- Ahmet YILDIRIM -- gmx-users

[gmx-users] deprotonation and DNA

Hi, I am running DNA simulation with amber force field. I did deprotonation on some of adenine group and then add some ions to get system without charge. Do you think this system will be suitable for MD simulation? regards, Jinghui -- gmx-users mailing listgmx-users@gromacs.org http://li

[gmx-users] Problem regarding Gromacs - GPU

Dear All, I have some queries regarding the benchmarking result of mdrun-gpu : 1. I have run mdrun-gpu with dhfr-impl-1nm.bench on tesla-c1060 , can you provide me the details regarding the execution time it takes as in my case it is running from a very long time (4-5 hours) . 2. Similar things a

Re: [gmx-users] protein folding

I think you can produce a loop of 42 aminoacids by using PYMOL software,It can produce a loop and it's result is a pdb file. Besides,when you could produce your loop you can use it in your folding process.because it is affected by other parts of protein as you said. I think this can be a good appro

Re: [gmx-users] protein folding

Dear All Thanks for your guidnces and specially for this website. On Tue, Nov 23, 2010 at 3:32 AM, Lutz Maibaum wrote: > On Nov 22, 2010, at 3:09 AM, mohsen ramezanpour wrote: > > I am searching for a tutorial for learning how to do protein folding > with Gromacs. > > Do any one know such tutori