Re: [gmx-users] Installation error (gromac4.0.5)

On Oct 5, 2009, at 16:01 , Justin A. Lemkul wrote: /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse- linux/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/CHPC/home/chpc/Test/oscar/ gromacs-4.0.5/src/ke

[gmx-users] Z-position calculation

Dear all,     I want to calculate the vertical position (Z-axis) of different lipid head groups as a function of time.     Looking forward for any suggestion.     Thanks in advance, Moutusi Manna Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com

Re: [gmx-users] Z-position calculation

g_traj with an index and playing with the different options. On Oct 6, 2009, at 11:01 AM, Moutusi Manna wrote: Dear all, I want to calculate the vertical position (Z-axis) of different lipid head groups as a function of time. Looking forward for any suggestion.

[gmx-users] Inter- and intra-molecular rdfs

Dear GMXers, I want to calculate the inter- and intra-molecular radial distribution functions (rdfs), separately. However, I find the g_rdf routine can only be useful to calculate the total rdf. Is there any similar routine which can be used to reach my aim? Please give me some hints. Thanks

[gmx-users] S-type Hydrogen bond correlation function

Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. Rama ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] S-type Hydrogen bond correlation function

Ramachandran G wrote: Dear gromacs users: I like to know whether gromacs will calculate S-type hydrogen bond correlation function? If it so how it can be done? Thank you. What does that mean? Rama ___ gmx-users mailing listgmx-users@grom

Re: [gmx-users] 256 DPPC bilayer

Dear Justin, Thanks. Ram On Mon, Oct 5, 2009 at 7:30 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> I am looking for a DPPC bilayer system of 256 and above , can anybody >> suugest me the site from where I can download Please... >> > > Take a pre-equilibrated 12

Re: [gmx-users] S-type Hydrogen bond correlation function

C_HB(T) = / S_HB(T) = / h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T, = 0, othe

Re: [gmx-users] Z-position calculation

Hi, You could also try g_bundle -z, it might do what you want. Cheers Tom --On Tuesday, October 06, 2009 11:04:29 +0200 XAvier Periole wrote: g_traj with an index and playing with the different options. On Oct 6, 2009, at 11:01 AM, Moutusi Manna wrote: Dear all, I want

Re: [gmx-users] S-type Hydrogen bond correlation function

Ramachandran G wrote: C_HB(T) = / S_HB(T) = / h(T) = 1, if a pair of atoms bonded at time T, = 0, otherwise H(T) = 1, if a pair of atoms continously bonded between time 0 to time T,

R: Re: R: RE: R: RE: R: RE: R:[gmx-users] Tabulated potential - Problem

Hi, Here's my mdp file: *+ title= Martini integrator = md tinit= 0.0 dt = 0.03 nsteps = 20 nstcomm = 1 nstxout = 1000 nstvout

[gmx-users] step 0Segmentation fault

Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less than 1000 during the l

Re: [gmx-users] step 0Segmentation fault

ram bio wrote: Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less tha

Re: [gmx-users] step 0Segmentation fault

Dear Justin, Thanks for the advice. I am using the DPPC 128 lipid bilayer from D. Peter Tieleman website, and the nvt.mdp file and the nvt.log files are as follows as in your tutorial: _

RE: [gmx-users] Z-position calculation

Hi, To get the z coordinate of the center of mass of a molecule I use the following command: echo "number of molecule" | g_traj -f xxx.xtc -s xxx.tpr -n xxx.ndx -nox -noy -com -ox xxx.xvg I guess you can create an .ndx file for a lipid head group to get the z coordinate of this. Regards, Sa

Re: [gmx-users] step 0Segmentation fault

ram bio wrote: Dear Justin, Thanks for the advice. I am using the DPPC 128 lipid bilayer from D. Peter Tieleman website, and the nvt.mdp file and the nvt.log files are as follows as in your tutorial: Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (st

[gmx-users] Dealing with non-aminoacid residues

Hi all, I'm looking to perform simulations on a series of synthetic co-polymers containing a variety of building blocks. I will be testing different sequences of the monomers, therefore I am looking for a way to streamline the generation of the topologies. I have been reading Chapter 5 of the

[gmx-users] Invitation to connect on LinkedIn

LinkedIn Ajani haresh requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Ajani Accept invitation from Ajani haresh http://www.linkedin.com/e/Xl9gjr6GAOlB4vIjeR9gqTUPRTl

[gmx-users] problems with gromacs preprocessor

Dear All, when I want to use grompp program grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr I got the following error message Fatal error: [ file "spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) So I tried to modify the topology file b

[gmx-users] problems with gromacs preprocessor

Dear All, when I want to use grompp program grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr I got the following error message Fatal error: [ file "spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) So I tried to modify the topology file b

[gmx-users] problems with gromacs preprocessor

Dear All, when I want to use grompp program grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr I got the following error message Fatal error: [ file "spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) So I tried to modify the topology file b

Re: [gmx-users] step 0Segmentation fault

Dear Justin, As suggested, when i reexamined the system.gro (protein_newbox + dppc128) one of the ends of the problem (as i think) i.e. few aminoacids of protein were beyond the water surface of the bilayer, probably this may be the reason for the presence of water molecules to the side of the bil

Re: [gmx-users] Dealing with non-aminoacid residues

Hi Pablo, I would write .rtp entries and so on for each monomer. You copy the modified files into your working directory. Have a great day, Andrea 2009/10/6 Englebienne, P. > Hi all, > > > > I’m looking to perform simulations on a series of synthetic co-polymers > containing a variety of bui

Re: [gmx-users] problems with gromacs preprocessor

There is no need to post three times in five minutes. If someone has advice, they will attend to your post in due time. This issue is commonly reported. Making haphazard changes to your topology is a bad idea. Please search the list archive (available through the interface at the Gromacs

Re: [gmx-users] step 0Segmentation fault

ram bio wrote: Dear Justin, As suggested, when i reexamined the system.gro (protein_newbox + dppc128) one of the ends of the problem (as i think) i.e. few aminoacids of protein were beyond the water surface of the bilayer, probably this may be the reason for the presence of water molecules to

Re: [gmx-users] Targeted Molecular Dynamics Simulation

Hi! I never used TMD, but this homepage (and the mail address on it) might help you: http://markt.bph.rub.de/~juergen/ Greets, Christian. Am Freitag, den 02.10.2009, 11:52 +0530 schrieb sanja...@iitb.ac.in: > I want to simulate a comformation change of a protein from state A to B. > >Fr

[gmx-users] pdb2gmx problem

Hello everyoneI am going to analysis the PDB file 3GJN.pdb.After giving the pdb2gmx it shows the fatal error "chain identifier 'B' was used in two non-sequential blocks (residue 404, atom 3227)".So what is the solution for this. Thank you Abhijit __

Re: [gmx-users] pdb2gmx problem

abhijit kayal wrote: Hello everyone I am going to analysis the PDB file 3GJN.pdb.After giving the pdb2gmx it shows the fatal error "chain identifier 'B' was used in two non-sequential blocks (residue 404, atom 3227)".So what is the solution for this. The error message i

Re: [gmx-users] pdb2gmx problem

Hi Abhijit, I think the Zinc ion goes with chain B and uses the same identifier. Given the fact that you didn't quite understand the error, and found it necessary to post a question, this raises another question: should you be wanting to simulate a protein with a zinc ion? (http://www.gromacs.org/

Re: [gmx-users] Inter- and intra-molecular rdfs

wuxiao wrote: > Dear GMXers, > I want to calculate the inter- and intra-molecular radial distribution > functions (rdfs), separately. However, I find the g_rdf routine can only > be useful to calculate the total rdf. Is there any similar routine which > can be used to reach my aim? Please give

Re: [gmx-users] Dealing with non-aminoacid residues

Englebienne, P. wrote: Hi all, I’m looking to perform simulations on a series of synthetic co-polymers containing a variety of building blocks. I will be testing different sequences of the monomers, therefore I am looking for a way to streamline the generation of the topologies. I hav

[gmx-users] PenG/CepC OPLSAA

Dear All, I would like to work on the R61 DD-peptidase enzyme complexed with penicillin G and cephalosporin C. The antibiotics are covalently bound and up till now I used gromacs/oplsaa for simulations on the apo enzyme but I'm struggling with the FF parametrization of the antibiotics. Ca

Re: [gmx-users] PenG/CepC OPLSAA

abelius wrote: Dear All, I would like to work on the R61 DD-peptidase enzyme complexed with penicillin G and cephalosporin C. The antibiotics are covalently bound and up till now I used gromacs/oplsaa for simulations on the apo enzyme but I'm struggling with the FF parametrization of the

Re: [gmx-users] S-type Hydrogen bond correlation function

Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: -

[gmx-users] Snapshot taken under certain condition

Dear users, Is there a way(in the mdp file) to take a snapshot of only the C-alpha atoms along a trajectory if certain condition are met(tested every time a snapshot needs to be taken) ? Thanks Arik ___ gmx-users mailing listgmx-users@gromacs.o

Re: [gmx-users] Snapshot taken under certain condition

Arik Cohen wrote: Dear users, Is there a way(in the mdp file) to take a snapshot of only the C-alpha atoms along a trajectory if certain condition are met(tested every time a snapshot needs to be taken) ? No, but you could probably script it after the trajectory is run, using whatever a

Re: [gmx-users] Snapshot taken under certain condition

Thanks for all your help and rapid response. Arik Justin A. Lemkul wrote: Arik Cohen wrote: Dear users, Is there a way(in the mdp file) to take a snapshot of only the C-alpha atoms along a trajectory if certain condition are met(tested every time a snapshot needs to be taken) ? No, bu

RE: [gmx-users] problems with gromacs preprocessor

> Dear All, > > when I want to use grompp program > grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o > minimbrady.tpr > > I got the following error message > > Fatal error: > [ file "spc.itp", line 41 ]: > Atom index (1) in settles out of bounds (1-0) > > So I tried to m

[gmx-users] problem when install gromacs on a node of cluster

Hey all, I wanted to install gromacs on one node of a cluster. Firstly I downloaded all needed packages to /home/william/software, then unpack all of them under this folder. Then, I followed the " Quick and Dirty Installation" instruction using following commands: export SOFT=$HOME

Re: [gmx-users] problem when install gromacs on a node of cluster

Santan William wrote: Hey all, I wanted to install gromacs on one node of a cluster. Firstly I downloaded all needed packages to /home/william/software, then unpack all of them under this folder. Then, I followed the " Quick and Dirty Installation" instruction using following

Re: [gmx-users] Snapshot taken under certain condition

Arik Cohen wrote: Dear users, Is there a way(in the mdp file) to take a snapshot of only the C-alpha atoms along a trajectory if certain condition are met(tested every time a snapshot needs to be taken) ? If you know in advance you'll only ever want the C-alpha atoms for analysis (dangerous

Re: [gmx-users] Snapshot taken under certain condition

Thanks allot for all your help Arik Mark Abraham wrote: Arik Cohen wrote: Dear users, Is there a way(in the mdp file) to take a snapshot of only the C-alpha atoms along a trajectory if certain condition are met(tested every time a snapshot needs to be taken) ? If you know in advance you'l

[gmx-users] Add new post-processing features in Gromacs

Dears, I would like to know if the details of how to add new post-processing features in Gromacs had been already discussed or described somewhere. I have in mind things like angle distribution, structure factor, and incoherent intermediate scattering function, to name a few, for glassy materials.

Re: [gmx-users] S-type Hydrogen bond correlation function

Ramachandran G wrote: Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below: You need to pass the -life option. --