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.

[gmx-users] Problem in equilibration for membrane system

Dear All, I'm running the protein complex with POPC system. NVT (100ps) and NPT (200ps) were done with restraint on the protein follow by 1000 ps of NPT without restraint on protein. The trajectory was checked in term of pressure, potential, area per lipid were checked and everything seems ok

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

I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote:

Re: [gmx-users] Problem in equilibration for membrane system

Bing Bing wrote: Dear All, I'm running the protein complex with POPC system. NVT (100ps) and NPT (200ps) were done with restraint on the protein follow by 1000 ps of NPT without restraint on protein. The trajectory was checked in term of pressure, potential, area per lipid were checked

Re: [gmx-users] Problem in equilibration for membrane system

My protein complex was minimized initially before putting into the lipid. POPC is also a preequilibrated structure from Tielemen website. I don't quite understand on what you meant by the protein is not happy with the restraint. The system went well through out the nvt, npt with restraint on

Re: [gmx-users] step 0Segmentation fault

Dear Justin, Thanks for the options suggested. I have used -princ and rotate 0 0 90 options with editconf and was able to place the protein vertically and at the centre of the DPPC bilayer (128 + 3655) from the site provided in the tutorial, but still the part of protein is outside the DPPC

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

Ramachandran G wrote: I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg -life koko.xvg To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van

Re: [gmx-users] step 0Segmentation fault

ram bio wrote: Dear Justin, Thanks for the options suggested. I have used -princ and rotate 0 0 90 options with editconf and was able to place the protein vertically and at the centre of the DPPC bilayer (128 + 3655) from the site provided in the tutorial, but still the part of protein is

Re: [gmx-users] Problem in equilibration for membrane system

Bing Bing wrote: My protein complex was minimized initially before putting into the lipid. POPC is also a preequilibrated structure from Tielemen website. I don't quite understand on what you meant by the protein is not happy with the restraint. The system went well through out the nvt, npt

[gmx-users] vsites and lincs-order

Hi, the manual suggests lincs-order = 6 when using large time steps (4-5 fs, with vsites). Has anyone experience how severe that issue is. Has anyone observed artefacts with lincs-order=4 and large time steps? Thanks a lot, Jochen -- --- Dr.

RE: [gmx-users] vsites and lincs-order

My P-Lincs paper http://dx.doi.org/10.1021/ct700200b shows that with order 6 and a time step of 4 fs you get roughly the same constraint accuracy and energy conservation as without v-sites and a 2 fs time step. With order 4 and a 4 fs time step the energy drift is 2.2 times higher than with

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

Tandia, Adama wrote: 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

Re: [gmx-users] vsites and lincs-order

All right, thanks! Since you mention energy conservation, maybe it would be worth adding notes or a warnings into pdb2gmx if the time step is large. First, if lincs-order is 4 (instead of 6) and second (more important), if nstlist is not reduced with increasing dt. I strongly feel that most

RE: [gmx-users] vsites and lincs-order

Date: Wed, 7 Oct 2009 15:51:00 +0200 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] vsites and lincs-order All right, thanks! Since you mention energy conservation, maybe it would be worth adding notes or a warnings into pdb2gmx if the time step is

[gmx-users] Extended structure for Estrogen receptor

Dear All, All the estrogen receptor alpha structure that I found on PDB repository, contain mainly the ligand binding domain (residues 301-550). I am looking for a structure that has the hinge region (240-300) as well. Does anyone have any extended structure (even if it is an engineered one) of

Re: [gmx-users] Extended structure for Estrogen receptor

Pradip Biswas wrote: Dear All, All the estrogen receptor alpha structure that I found on PDB repository, contain mainly the ligand binding domain (residues 301-550). I am looking for a structure that has the hinge region (240-300) as well. Does anyone have any extended structure (even if

[gmx-users] Distance restraint problem with 4.0.5 version

Hi Gmxers Some months ago I performed some simulations, with GMX 3.3.3 version, where I apply distance restraint between water oxygen atoms and a static dummy site located at the center of a sphere to keep waters inside this sphere. After performed an upgrade to GMX 4.0.5 version this

Re: [gmx-users] Extended structure for Estrogen receptor

Justin, I came to this board as a last resource, after failing in my search. Pradip On Wed, Oct 7, 2009 at 9:09 AM, Justin A. Lemkul jalem...@vt.edu wrote: Pradip Biswas wrote: Dear All, All the estrogen receptor alpha structure that I found on PDB repository, contain mainly the ligand

[gmx-users] PRODRG

Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an error message that states: DRG is not in the topology database. I have tried to use the available tutorial to solve this issue, but with not much success.

Re: [gmx-users] PRODRG

Smith, Chanel Chonda wrote: Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an error message that states: DRG is not in the topology database. I have tried to use the available tutorial to solve this issue,

Re: [gmx-users] PRODRG

Hello Chanel Could you send a copy of the PDB file. I think that the error is related with label atoms included in each force fiel parameter. See you. Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an

Re: [gmx-users] PRODRG

jorge_quint...@ciencias.uis.edu.co wrote: Hello Chanel Could you send a copy of the PDB file. I think that the error is related with label atoms included in each force fiel parameter. More likely this is yet another case of a common misconception about how to use Gromacs. Specifically,

[gmx-users] mailing list search

Hello I have been trying to search the mailing list after I logged in to the new gromacs website. But I do not get any searched results but This page is restricted. comment. Could anyone tell me what the problem might be? Thank you Sunjoo ___

[gmx-users] Problems with FENE potential

Hi there, I have been trying to run a simulation using the fene potential option in a chain of beads as model for my protein, ubiquitin and the sd integrator. The problem comes when one of the beads goes beyond the limits and comes out from the other side of the box, the distance comes out

Re: [gmx-users] mailing list search

Hi, I made some updates and incorrectly changed the permissions. You should be able to search now even without logging in. Rossen Sun Joo Lee wrote: Hello I have been trying to search the mailing list after I logged in to the new gromacs website. But I do not get any searched results but

[gmx-users] Snapshots in different files

Dear users, Is there a way to take a snapshot along the trajectory and write it into a different file, so that each snapshot will be written into its own file named with its own index ?(e.g. snap_1, snap_2 ) Thanks Arik ___ gmx-users mailing

Re: [gmx-users] Snapshots in different files

Arik Cohen wrote: Dear users, Is there a way to take a snapshot along the trajectory and write it into a different file, so that each snapshot will be written into its own file named with its own index ?(e.g. snap_1, snap_2 ) trjconv -sep -Justin Thanks Arik

Re: [gmx-users] Snapshots in different files

Thanks allot, but isn't trjconv should be executed after the trajectory has finished ?. I would like to put each snapshot in a different file on the fly. Thanks Arik Justin A. Lemkul wrote: Arik Cohen wrote: Dear users, Is there a way to take a snapshot along the trajectory and write

Re: [gmx-users] Extended structure for Estrogen receptor

Pradip Biswas wrote: Dear All, All the estrogen receptor alpha structure that I found on PDB repository, contain mainly the ligand binding domain (residues 301-550). I am looking for a structure that has the hinge region (240-300) as well. Does anyone have any extended structure (even if it

Re: [gmx-users] Snapshots in different files

Arik Cohen wrote: Thanks allot, but isn't trjconv should be executed after the trajectory has finished ?. I would like to put each snapshot in a different file on the fly. Not possible, as far as I'm aware. -Justin Thanks Arik Justin A. Lemkul wrote: Arik Cohen wrote: Dear

Re: [gmx-users] Snapshots in different files

Arik Cohen wrote: Thanks allot, but isn't trjconv should be executed after the trajectory has finished ?. I would like to put each snapshot in a different file on the fly. As Justin said, you can't do that. For starters, it consumes vast amounts of disk. Also, it doesn't take long to do it

Re: [gmx-users] Snapshots in different files

Thanks allot for all your help and ultrafast response. Arik Justin A. Lemkul wrote: Arik Cohen wrote: Thanks allot, but isn't trjconv should be executed after the trajectory has finished ?. I would like to put each snapshot in a different file on the fly. Not possible, as far as I'm

Re: [gmx-users] Snapshots in different files

Thanks for answering. This would not be the case so much since another program(sniffer) can be working along side gromacs examining each snapshot(Max 400 residues == atoms. I'm only interested in the C-alpha) and then if all criteria are met to extract/or save the coor and if not to erase the

[gmx-users] trjconv to process multiple types of molecules

Hi There, I have a problem using trjconv to get the trajectory. I have three types of molecules: MOL, ION, SOL and I want to convert only 2 types of them, how ever trjconv seems only accept one input. I want to keep only MOL and ION, and avoid the large amount of SOL, which will reduce the

Re: [gmx-users] trjconv to process multiple types of molecules

Hi, You need to use make_ndx to merge the MOL and ION into a new index group and then use that group in trjconv Cheers Tom --On 07 October 2009 15:32 -0700 Yan Gao y1...@ucsd.edu wrote: Hi There, I have a problem using trjconv to get the trajectory. I have three types of molecules: MOL,

Re: [gmx-users] trjconv to process multiple types of molecules

Yan Gao wrote: Hi There, I have a problem using trjconv to get the trajectory. I have three types of molecules: MOL, ION, SOL and I want to convert only 2 types of them, how ever trjconv seems only accept one input. I want to keep only MOL and ION, and avoid the large amount of SOL, which

Re: [gmx-users] Distance restraint problem with 4.0.5 version

Alexandre Suman de Araujo wrote: Hi Gmxers Some months ago I performed some simulations, with GMX 3.3.3 version, where I apply distance restraint between water oxygen atoms and a static dummy site located at the center of a sphere to keep waters inside this sphere. After performed an upgrade

Re: [gmx-users] Problem in equilibration for membrane system

hi Bing, I advice you to look carefully on any clashes between POPC and the protein. It might happen that one lipid was 'trapped' inside the protein or more likely that atom water had trapped and that what crash you system. Cheers, Itamar --- In theory, there is no difference between theory

RE: [gmx-users] Snapshots in different files

If the time frame between snapshots is not too short, you could have that as the length of each MD run, then simple extend the run to keep on going. Could be a bit inefficient. (This is how you should run MD anyway, to ensure don't lose a lot of information if the computer system you are running

[gmx-users] g_dipole for spce

Dear all, I tried to use g_dipole for a SPC/E water system and I got these results. - Dipole moment (Debye) - Average = 2.3506 Std. Dev. = 0.0143 Error = 0.0001 The following averages for the complete trajectory have been

[gmx-users] user defined potential function for 1-4 interaction

Hi All: I have two separate problems for this subject. 1) What should be the way to pass a formatted table for the 1-4 interaction for two different groups? Reading page 150 and 180 of manual 4.0, I understand user defined potential functions can be passed for many groups using

[gmx-users] g_current

Does anyone know of a reference (besides the manual) for the calculations performed by g_current? Thank you, Andrew ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] How does x2top clean dihedrals?

Dear all, Sorry that I have to post this message similar to one posted several days ago, for I have spent much time on thinking about it but still have not got a credible explanation. I use x2top to get topology of a capped carbon nanotube with 168 atoms using oplsaa force field. The

RE: [gmx-users] PRODRG

In the drug-enzyme tutorial it says that the crude was refined using a certain force field, SD, and CG. How was this accomplished? -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Wed 10/7/2009 1:11 PM To: Discussion list for GROMACS users

[gmx-users] Optimizing a parallel simulation

Hi There, While running a parallel MD simulation, I got following message while playing with parameters: NOTE 3 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance,