Re: [gmx-users] Re: do_dssp

Yes , I am using the correct options for dssp. But still I am getting the same error. On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham wrote: > On 5/04/2012 10:25 AM, bharat gupta wrote: > >> Hi, >> >> I am trying to plot the ss content using the do_dssp command , but I am >> getting the following er

[gmx-users] Atom N not found....

Hi Gromacs friends, When I given the command ... pdb2gmx -f .. -o .. -p .. -ignh I gate the following error.. -- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1070 Fatal error: atom N n

Re: [gmx-users] Re: do_dssp

On 5/04/2012 10:25 AM, bharat gupta wrote: Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 > /dev/null 2> /dev/null I am using the DSSPold version. What could

Re: [gmx-users] on a on-line command for

On 5/04/2012 2:07 PM, Acoot Brett wrote: Dear All, In http://www-personal.umich.edu/~amadi/fwspidr_tutor.pdf , there is a command *tpbconv -f *traj.trr *-s *topol.tpr *-e *ener.edr *-o *tpxout.tpr *--until *$VALUE But we know we never

Re: [gmx-users] Further discussion: the -extend function of the tpbconv command

On 5/04/2012 1:58 PM, Acoot Brett wrote: Dear All, According to "http://www.gromacs.org/Documentation/How-tos/Extending_Simulations"; , the commands for extending MD are: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt But if you read "http://www

[gmx-users] on a on-line command for

Dear All,   In http://www-personal.umich.edu/~amadi/fwspidr_tutor.pdf, there is a command   tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr –until $VALUE   But we know we never have the topol.tpr as I know.   Will you please give a clarification?   Cheers,   Acoot   -- gmx-users mailin

[gmx-users] Further discussion: the -extend function of the tpbconv command

Dear All,   According to "http://www.gromacs.org/Documentation/How-tos/Extending_Simulations" , the commands for extending MD are:     tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt But if you read "http://www.gromacs.org/Documentation/File_Format

[gmx-users] which xtc file should be used for the trjconv command

Dear All,   In the on-line tutorial on lysozyme (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html), there is a command   trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact   Will you please consider in that command whether

[gmx-users] Re: do_dssp

Hi, I am trying to plot the ss content using the do_dssp command , but I am getting the following error :- Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn ddXN9mH0 > /dev/null 2> /dev/null I am using the DSSPold version. What could be the possible reason for such an error ?? Re

Re: [gmx-users] Velocity autocorrelation

On Apr 4, 2012, at 1:16 PM, Ignacio Fernández Galván wrote: > --- On Sun, 1/4/12, Ignacio Fernández Galván wrote: > >> Maybe instead of individual atoms, I should analyze the VACF >> of the center of mass of each molecule, and the rotational >> ACF. The latter I know how to do it. Is there an

Re: [gmx-users] Re: Simulation in the high temperature conditions

James Starlight wrote: Justin, 1) I've defined 5 steps for specified definition of the time of each step as well as for more flexibile controle of the such annealing: e.g I want that equilibration step corresponded to the temperature between 320 and 330K will be longer than between first s

Re: [gmx-users] Re: Simulation in the high temperature conditions

Justin, 1) I've defined 5 steps for specified definition of the time of each step as well as for more flexibile controle of the such annealing: e.g I want that equilibration step corresponded to the temperature between 320 and 330K will be longer than between first step corresponded to 300-310K e

Re: [gmx-users] Re: Simulation in the high temperature conditions

James Starlight wrote: Justin,thanks! 1) For example for the situation presented in manual for 2 groups with 3 and 4 points the time enty should be annealing_time = 0 3 6 0 2 4 6 from this I've understood that 0 value is the start of timer for each group and subsequent values are the act

Re: [gmx-users] Re: Simulation in the high temperature conditions

Justin,thanks! 1) For example for the situation presented in manual for 2 groups with 3 and 4 points the time enty should be annealing_time = 0 3 6 0 2 4 6 from this I've understood that 0 value is the start of timer for each group and subsequent values are the actual time in the ps, havennt it

Re: [gmx-users] do_dssp

Bernhard Knapp wrote: The problem with this solution is that I would have to recompile gromacs on all maschines were I want to use dssp, right? Is there an older version of dssp still available from somewhere? On the dssp-homepage I found unfortunatly only the current but no past versions of

[gmx-users] Re: gmx-users Digest, Vol 96, Issue 30

The problem with this solution is that I would have to recompile gromacs on all maschines were I want to use dssp, right? Is there an older version of dssp still available from somewhere? On the dssp-homepage I found unfortunatly only the current but no past versions of dssp... best, Bernhard

Re: [gmx-users] File editing - only one layer of water around a molecule

On 4/04/2012 7:27 PM, Lara Bunte wrote: Hello I have a question about editing a pdb file. I have a molecule in a box of water as a pdb file. I want to remove all water except of ONE layer around he molecule. How to do that? Do you know a software that is able to do that? Do you know how it

Re: [gmx-users] do_dssp

On 4/04/2012 10:02 PM, Justin A. Lemkul wrote: Bernhard Knapp wrote: Hi I have some problems to get do_dssp running: I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I copied it to the correct location: "c

Re: [gmx-users] Re: Simulation in the high temperature conditions

James Starlight wrote: So if it were not quite clearly :) my main question is about methodology of such gradually temperature rise in the nvt enssemble conditions. Might it be realised by means of simple equilibation in one mdp file varying some parametries to change time-step of temperatu

Re: [gmx-users] do_dssp

Bernhard Knapp wrote: Hi I have some problems to get do_dssp running: I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I copied it to the correct location: "cp dssp-2-linux-i386 /usr/local/bin/dssp" and ga

Re: AW: [gmx-users] Shape of box

Rausch, Felix wrote: Hi Lara, Please see "editconf -h" for the available box shapes. Which of these you use is depending on your system (or a matter of taste actually). The dodecahedron is mostly used to decrease the system volume, thus it's a good choice for the simulation of a single protein

Re: [gmx-users] Bad box in protein.gro

sai nitin wrote: Hi all, I recently started molecular dynamics with gromacs performing protein-ligand simulations for my project first i worked out example from justin tutorials on protein ligand system and trying to apply to my protein and ligand. First i generated topology for my protei

[gmx-users] Re: Simulation in the high temperature conditions

So if it were not quite clearly :) my main question is about methodology of such gradually temperature rise in the nvt enssemble conditions. Might it be realised by means of simple equilibation in one mdp file varying some parametries to change time-step of temperature growth? Or this methodology

Re: [gmx-users] Velocity autocorrelation

--- On Sun, 1/4/12, Ignacio Fernández Galván wrote: > Maybe instead of individual atoms, I should analyze the VACF > of the center of mass of each molecule, and the rotational > ACF. The latter I know how to do it. Is there an "easy" way > to calculate the former? Silly me, I should have tried t

[gmx-users] do_dssp

Hi I have some problems to get do_dssp running: I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I copied it to the correct location: "cp dssp-2-linux-i386 /usr/local/bin/dssp" and gave the user the right to e

AW: [gmx-users] Shape of box

Hi Lara, Please see "editconf -h" for the available box shapes. Which of these you use is depending on your system (or a matter of taste actually). The dodecahedron is mostly used to decrease the system volume, thus it's a good choice for the simulation of a single protein in solvent (as in your

[gmx-users] File editing - only one layer of water around a molecule

Hello I have a question about editing a pdb file. I have a molecule in a box of water as a pdb file. I want to remove all water except of ONE layer around he molecule.  How to do that? Do you know a software that is able to do that? Do you know how it could work with programs like PyMol or o

[gmx-users] Shape of box

Hello If you add solvent water around your protein you have to generate a box with the editconf command. How to know what shape that box should have? In my tutorial is a dodecahedron used. What other boxes exist and how to know which box one has to use? Thanks Greetings Lara -- gmx-users mail

[gmx-users] Parallel run on multiple nodes

Dear GROMACS users, I'm a new user of GROMACS. The command "mpirun -np 8 mdrun" is working well in a node with 8 processors. Now I want to run GROMACS parallel on more processors, i.e., multiple nodes. I tried to use "mpirun -n 16 -host node018,node022 mdrun" (node018 and node022 each has 8 proce

[gmx-users] Bad box in protein.gro

Hi all, I recently started molecular dynamics with gromacs performing protein-ligand simulations for my project first i worked out example from justin tutorials on protein ligand system and trying to apply to my protein and ligand. First i generated topology for my protein using pdbgmx and then i

Re: [gmx-users] the -extend function of the tpbconv command

On 4/04/2012 6:24 PM, Acoot Brett wrote: Hi Justin and All, The on-line document on "Extending Simulations" writes, "You might want to use the -append option of mdrun to append the new output to the old files. Note that this will on

Re: [gmx-users] the -extend function of the tpbconv command

Hi Justin and All,   The on-line document on "Extending Simulations" writes,   "You might want to use the -append option of mdrun to append the new output to the old files. Note that this will only work when the old output files have not been modified by the user. Appending is the default behavi