Re: [gmx-users] ffgmx43a1 for use with lipids

Sumamohan S wrote: Hi Mark, I am currently using ffgmx force field but i want to try with G43a1 force field. People have used modified G43a1 force field for use with lipids in membrane protein simulations. Well if it already exists, you may need find the documentation and/or the mod

Re: [gmx-users] ffgmx43a1 for use with lipids

Hi Mark, I am currently using ffgmx force field but i want to try with G43a1 force field. People have used modified G43a1 force field for use with lipids in membrane protein simulations. - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent:

Re: [gmx-users] Simulated annealing

jayant james wrote: Hi! I have a question with regard to a system that I am attempting to model. The N-terminal of chain of the protein was not resolved crystallographically but was later solved by NMR. Now my plan is to append the NMR structure on to chain A of the protein and perform simula

[gmx-users] Simulated annealing

Hi! I have a question with regard to a system that I am attempting to model. The N-terminal of chain of the protein was not resolved crystallographically but was later solved by NMR. Now my plan is to append the NMR structure on to chain A of the protein and perform simulated annealing only for the

Re: [gmx-users] trjconv fit subset of atoms

Ok, I think I see what's going on now. If I have two different groups in the ndx file, I can then select between them for the different purposes. Sorry for the confusion. Josh On Feb 26, 2009, at 2:48 PM, Tsjerk Wassenaar wrote: Josh, -n indicates that groups are to be read from the ind

Re: [gmx-users] trjconv fit subset of atoms

Josh, -n indicates that groups are to be read from the index file, rather than using the standard groups. It's not related to what the group is being used for. Cheers, Tsjerk On Thu, Feb 26, 2009 at 11:34 PM, Joshua Adelman wrote: > I'm using 4.0.2. There are three optional ndx flags, -n -sub

Re: [gmx-users] trjconv fit subset of atoms

I'm using 4.0.2. There are three optional ndx flags, -n -sub -fr. As far as I can tell, -n defines the output group (will also set the fit group as the same), -sub tells you the frame numbers for cutting the trajectory into smaller sections and -fr also has something to do with frames. If y

Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

Sorry realised I posted the amber ATP link wrong, it is without the ) at the end: http://www.pharmacy.manchester.ac.uk/bryce/amber Tom --On Thursday, February 26, 2009 17:15:22 + TJ Piggot wrote: Some of these charges look a bit suspect to me (eg the charge on the gamma phosphate). If

Re: [gmx-users] ffgmx43a1 for use with lipids

Sumamohan S wrote: Dear Gromacs users, I want to do MD simulation of protein embedded in a POPC lipid bilayer using ffgmx43a1 force field. How can we modify ffgmx43a1 force field for use with lipids? or the modified forcefield is available anywhere? If this one isn't already

[gmx-users] buffer reading error with grompp

Hello, I'm trying to compile Gromacs-4.0.3 on one of our clusters in my local directory (the OS is CentOS release 4.2). The compilation only produces 3 warnings: pme.c:964: warning: dereferencing type-punned pointer will break strict-aliasing rules pppm.c:387: warning: dereferencing

Re: [gmx-users] trjconv fit subset of atoms

Hi Josh, When fitting, trjconv asks for separate groups for performing the fit and for the output. No need to hack anything. You can make a suitable index file using make_ndx. Cheers, Tsjerk On Thu, Feb 26, 2009 at 7:47 PM, Joshua Adelman wrote: > I am trying to use trjconv to generate a new .

RE: [gmx-users] trjconv fit subset of atoms

Hi, Which version of Gromacs are you using? In 4.0, but I think also in 3.3, trjconv ask for both a fit and an output group. Berk To: gmx-users@gromacs.org From: jadel...@berkeley.edu Date: Thu, 26 Feb 2009 10:47:38 -0800 Subject: [gmx-users] trjconv fit subset of atoms I am trying to use trj

[gmx-users] Re:Re: how to convert the *.cube file to a (x, y, z) format file

Hi, Thanks for your attention to gmxgrid, but discussion on the usage of gmxgrid is off-topic for this mailing list, I will answer your question privately. --Lu Tian > Message: 3 > Date: Thu, 26 Feb 2009 22:35:10 +0800 > From: "Jinyao Wang" > Subject: [gmx-users] Re:Re: how to convert the *.

[gmx-users] trjconv fit subset of atoms

I am trying to use trjconv to generate a new .xtc file in which all frames have been aligned based on a subset of atoms (e.g. I have a multi-domain protein and I want to align the trajectory to one of the domains). Using a standard .ndx file only outputs the atoms associated with the fitted

Re: [gmx-users] energy file

jayant james wrote: Hi! Thanks for your reply. I am having an on going simulation the md.log file states that it has written 875ps but the energy file data for only 662 ps!! this is brand new machine and is so there is no problem of running out of space. I am appending my pr.mdp file please

Re: [gmx-users] energy file

Hi! Thanks for your reply. I am having an on going simulation the md.log file states that it has written 875ps but the energy file data for only 662 ps!! this is brand new machine and is so there is no problem of running out of space. I am appending my pr.mdp file please take a look if its some thi

Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

Some of these charges look a bit suspect to me (eg the charge on the gamma phosphate). If you do not need to use OPLS then there is ATP included in the (united atom) gromos forcefields (see the top folder) and also ATP parameters available for the (all atom) Amber forcefields (see http://www.ph

Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela wrote: > Does anybody have the topology files for ATP and/or ADP for the OPLS-AA > forcefield?. If not, how can I parameterize this molecules?. > Best regards. >Lucio Montero. > > Lucio Ricardo Montero Valenzuela

[gmx-users] Re:Re: how to convert the *.cube file to a (x, y, z) format file

Hi Lu Tian , Thank you for your help. Your program is very useful for me. I have run it. But I have some puzzled for the output files. 1. Running the program for getting all the data with x,y,z,coordinates. I got four columns data in the output files? what is the fourth column if the

[gmx-users] ffgmx43a1 for use with lipids

Dear Gromacs users, I want to do MD simulation of protein embedded in a POPC lipid bilayer using ffgmx43a1 force field. How can we modify ffgmx43a1 force field for use with lipids? or the modified forcefield is available anywhere? Thanks in advance, Suma Jayakrishnan Amrita Sch

[gmx-users] PLUMED release 1.0.0 available

The PLUMED Developers Team is proud to announce that the PLUMED release 1.0.0 is available at http://merlino.mi.infn.it/plumed. PLUMED is a plugin for free-energy calculations in molecular systems. It can be interfaced, through a simple patch procedure, with some of the most popular classical mo

Re: [gmx-users] Please give me advises for the computing system.

Seungpyo Hong wrote: Dear Gromacs users, I am planning to buy a computer system for MD. But don't know much about hardware. Help me please! Currently we have three candidates with following list of CPUs: 1. Core2 Quad (Q9550) 2. Xeon (E5440) x 2 (2-way SMP system) 3. Core i7 (i7-920) We usual

Re: [gmx-users] problem in creating topol.tpr file

Read for yourself. Think for yourself. If we are to answer a question, we want to know that the receiver is capable of reading (the answer) and to comprehend (the answer). It's up to you to show that you are so capable (by showing you've read the output and thought it over) that answering your ques

Re: [gmx-users] problem in creating topol.tpr file

nitu sharma wrote: Dear All, I want to run the gromacs 4.0.3 but I am unable in creating topol.tpr file when I put the grommp command it shows error like this "Program grompp, VERSION 4.0.3 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (1), g

[gmx-users] problem in creating topol.tpr file

Dear All, I want to run the gromacs 4.0.3 but I am unable in creating topol.tpr file when I put the grommp command it shows error like this "Program grompp, VERSION 4.0.3 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (1), grompp terminated. If you a

Re: [gmx-users] problem in running gromacs demo

nitu sharma wrote: Dear all, I have successfully installed the gromacs 4.0.3 it is working but the problem is when I want to run the gromacs demo during processing when I put the command "grompp -v" the output like this ,:-) G R O M A C S (-:

[gmx-users] problem in running gromacs demo

Dear all, I have successfully installed the gromacs 4.0.3 it is working but the problem is when I want to run the gromacs demo during processing when I put the command "grompp -v" the output like this ,:-) G R O M A C S (-: Gromacs Runs On Most of

[gmx-users] Re: how to convert the *.cube file to a (x, y, z) format file

hi, My program gmxgrid can do this, have a try. http://sobereva.brinkster.net/gmxgrid.rar -- Lu Tian > hi gmx-users, > I have run g_spatial and got a *.cube output file. But I > don't know how to convert the *.cube file to a (x,y,z) > format file in order to load it into other plot software. >

RE: [gmx-users] combination rules -- the part aboutthecombinationrules

Hi, But do you need any other parameters than zinc and oxide? If not, you can simply remove all other parameters. If you need other atoms as well, you will need to find a consistent force field, probably or completely LJ or completely Buckingham. Berk > Date: Thu, 26 Feb 2009 09:22:26 +1100 >