[gmx-users] when using RB dihedral function, how to exclude 1-4 vdw ?

2009-11-20 Thread XunJie Yang
Hello GMX users: I'm new to GMX and I'm now facing a problem. For short, it is about how to properly use the RB function. I'm now doing simulation with AMBER force field(ported to GMX by FFAmber), which employs Ryckaert-Bellemans function for dihedral, it is how FFAmber forcefield treats dih

[gmx-users] when using RB dihedral function, how to exclude 1-4 vdw ?

2009-11-20 Thread XunJie Yang
Hello GMX users: I'm new to GMX and I'm now facing a problem. For short, it is about how to properly use the RB function. I'm now doing simulation with AMBER force field(ported to GMX by FFAmber), which employs Ryckaert-Bellemans function for dihedral, it is how FFAmber forcefield treats dih

Re: [gmx-users] when using RB dihedral function, how to exclude 1-4 vdw ?

2009-11-20 Thread Mark Abraham
XunJie Yang wrote: Hello GMX users: I'm new to GMX and I'm now facing a problem. For short, it is about how to properly use the RB function. I'm now doing simulation with AMBER force field(ported to GMX by FFAmber), which employs Ryckaert-Bellemans function for dihedral, it is how FFAmber fo

[gmx-users] Re: gmx-users Digest, Vol 67, Issue 110

2009-11-20 Thread Cun Zhang
Hi, Justin. Thank you for your help! I was intended to reply the third question after I retryed the simulation under your advice,but I haven't enough time to do it. It's too late :) Just now, I do a simulation. All seems ok. I will check it again. Thank you again! Cun Zhang > >pymol b4em.pdb #

[gmx-users] Re: gmx-users Digest, Vol 67, Issue 110 (How to make carbon nanotube infinite?)

2009-11-20 Thread Justin A. Lemkul
Cun Zhang wrote: Hi, Justin. Thank you for your help! I was intended to reply the third question after I retryed the simulation under your advice,but I haven't enough time to do it. It's too late :) Just now, I do a simulation. All seems ok. I will check it again. Thank you again! Cun Zhan

Re: [gmx-users] when using RB dihedral function, how to exclude 1-4 vdw ?

2009-11-20 Thread TJ Piggot
If you read this part of the manual again you will see that it discusses this point of 1-4 interactions for the OPLS forcefield and RB dihedrals (and the same as discussed for OPLS is true for the AMBER forcefields using RB potentials for dihedrals). Tom --On Friday, November 20, 2009 16:45:

[gmx-users] RE:How to check for bad contacts.

2009-11-20 Thread Lum Nforbi
Hello Dr. Warren, Thank you for the useful information. I did use vmd to view my molecule, but in a system of 2000 molecules, it is quite difficult to locate atom 2065 (an O atom) which is actually the offending atom. I have described the way I did the work below. I used a random generator softwar

[gmx-users] Disulfide bridge formation between A and B state

2009-11-20 Thread Jochen Hub
Hi, I have yesterday already started a topic, but I think I was a bit unclear about what is the problem. I want to have a disulfide bridge in the B state, but not in the A state. And I have not found a way to get the Coulomb interaction between the two sulfurs (and other nearby atoms) right

[gmx-users] g_saltbr

2009-11-20 Thread Sarah Witzke
Dear gromacs users, First of all thank you for all your previous help! I have a new question regarding an analysis of ionic interactions between DMPC lipids and a small molecule with a deprotonated carboxylic acid. g_saltbr takes as input an .xtc file and a .tpr file and from these files it mea

Re: [gmx-users] RE:How to check for bad contacts.

2009-11-20 Thread Justin A. Lemkul
Lum Nforbi wrote: Hello Dr. Warren, Thank you for the useful information. I did use vmd to view my molecule, but in a system of 2000 molecules, it is quite difficult to locate atom 2065 (an O atom) which is actually the offending atom. I have described the way I did the work below. I used a

Re: [gmx-users] RE:How to check for bad contacts.

2009-11-20 Thread Mark Abraham
Lum Nforbi wrote: Hello Dr. Warren, Thank you for the useful information. I did use vmd to view my molecule, but in a system of 2000 molecules, it is quite difficult to locate atom 2065 (an O atom) which is actually the offending atom. I have described the way I did the work below. I used a

Re: [gmx-users] g_saltbr

2009-11-20 Thread Justin A. Lemkul
Sarah Witzke wrote: Dear gromacs users, First of all thank you for all your previous help! I have a new question regarding an analysis of ionic interactions between DMPC lipids and a small molecule with a deprotonated carboxylic acid. g_saltbr takes as input an .xtc file and a .tpr file and

RE: [gmx-users] Disulfide bridge formation between A and B state

2009-11-20 Thread Berk Hess
Hi, I would say that it is very uncommon to form a bond during free energy calculations. To make this work easily we would need to introduce a pair interaction with all parameters explicit that can be perturbed. For the moment you should be able to get it to work using tabulated bonded inter

RE: [gmx-users] g_saltbr

2009-11-20 Thread Sarah Witzke
-Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Fri 20-11-2009 14:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_saltbr Sarah Witzke wrote: > Dear gromacs users, > > First of all thank you for all your previous help! >

Re: [gmx-users] Hydrated radius of ions

2009-11-20 Thread Manik Mayur
2009/11/20 Dallas B. Warren > g_rdf ? > Thanks, but while using g_rdf, when I have lots of ions, do I have to make an ndx file entry of a single ion or I have to supply the whole ion group while selecting the reference group. > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dy

[gmx-users] Pushing MD further

2009-11-20 Thread Thielges, Sabine
Hi, I am currently running some GPRC MD with membrane. After a lot of trial I now have a nice 25 ns run with an agonist. But the final structure is too close the starting and I know it is far from what the biology describes. I would like to know if there is options that I can add to my md.mdp fil

Re: [gmx-users] Disulfide bridge formation between A and B state

2009-11-20 Thread Jochen Hub
Hi Berk, thanks a lot for the comment. Actually I have found a solution which is good enough for what I am planing to do. I have placed a dummy onto the sulfur which is turned on while the sulfur is tuned off. And I switch on a bond between the dummys when switching from A to B. Then I have a

Re: [gmx-users] Pushing MD further

2009-11-20 Thread Justin A. Lemkul
Thielges, Sabine wrote: Hi, I am currently running some GPRC MD with membrane. After a lot of trial I now have a nice 25 ns run with an agonist. But the final structure is too close the starting and I know it is far from what the biology describes. I would like to know if there is options tha

RE: [gmx-users] Pushing MD further

2009-11-20 Thread Berk Hess
Hi, I would think any system with a membrane in it is too large to gain much with REMD (unless you are interested in the temperature dependence). You can use essential dynamics sampling or flooding, see make_edi. Berk > Date: Fri, 20 Nov 2009 10:00:11 -0500 > From: jalem...@vt.edu > To: gmx-u

RE: [gmx-users] Pushing MD further

2009-11-20 Thread TJ Piggot
I would also add that you could also use TEE-REX which overcomes some of the problems associated with normal REMD on large systems. Do note that as far as i know the TEE-REX patch only works with GROMACS versions 3.3.x and so each replica in the TEE-REX simulation can only be ran on one CPU, me

[gmx-users] problems compiling gromacs 4.0.5 in Ubuntu 9.0.4

2009-11-20 Thread pedro alberto valiente flores
Hi: I ' am trying to compile gromacs 4.0.5 in Ubuntu 9.0.4 I use the following command line in the configure script ./configure --enable-mpi --program-suffix=_405_mpi --prefix= $HOME/software/gmx405 MPICC=$HOME/software/openmpi-1.2.8/bin/mpicc CPPFLAGS="-I$HOME/software/openmpi-1.2.8/include/ -I$

[gmx-users] gromacs with gaussian 09

2009-11-20 Thread ilona . baldus
Hello, Has anyone amongst you tried if the Gaussian implementation also works for Gaussian 09? We were considering to get it, but it only makes sense for us if we can use it for Gromacs-Gaussian qmmm calculations. Have you experienced any other obstacles than variables being renamed? Chee

[gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

2009-11-20 Thread Yanmei Song
Dear Users: Anyone knows how to get the standard errors of the results based on block averaging from non-equilibrium MD simulations? I am trying to get the error estimations for my calculated viscosity of the fluid. Any command can give me that? or I have to do it manually? Thank you in advance!

Re: [gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

2009-11-20 Thread Justin A. Lemkul
Yanmei Song wrote: Dear Users: Anyone knows how to get the standard errors of the results based on block averaging from non-equilibrium MD simulations? I am trying to get the error estimations for my calculated viscosity of the fluid. Any command can give me that? or I have to do it manuall

Re: [gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

2009-11-20 Thread Yanmei Song
Dear Justin: I really appreciate your response and help! I am confusing about the result by using this method. I found in B. Hess's paper (Appendix, JCP, 116, 2002) that " this gives a standard error estimate for 1/eta of 29.5. "; and the error he gives for that eta is 0.006. I thought the error

Re: [gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

2009-11-20 Thread Justin A. Lemkul
Yanmei Song wrote: Dear Justin: I really appreciate your response and help! I am confusing about the result by using this method. I found in B. Hess's paper (Appendix, JCP, 116, 2002) that " this gives a standard error estimate for 1/eta of 29.5. "; and the error he gives for that eta is

Re: [gmx-users] problems compiling gromacs 4.0.5 in Ubuntu 9.0.4

2009-11-20 Thread Mark Abraham
pedro alberto valiente flores wrote: Hi: I ' am trying to compile gromacs 4.0.5 in Ubuntu 9.0.4 I use the following command line in the configure script ./configure --enable-mpi --program-suffix=_405_mpi --prefix= $HOME/software/gmx405 MPICC=$HOME/software/openmpi-1.2.8/bin/mpicc CPPFLAGS="-I$HO

Re: [gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

2009-11-20 Thread Yanmei Song
Dear Justin: Thank you so much for your quick response. But I still don't get it. Should I calculate the standard error manually by using the equations A17 (in B. Hess' s paper) after I get the result by g_analyze. And then which value I should use for the sigma? Here is the output : invalid fi

Re: [gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

2009-11-20 Thread Justin A. Lemkul
Yanmei Song wrote: Dear Justin: Thank you so much for your quick response. But I still don't get it. Should I calculate the standard error manually by using the equations A17 (in B. Hess' s paper) after I get the result by g_analyze. And then which value I should use for the sigma? Here i

[gmx-users] error in converting charmm to gromacs

2009-11-20 Thread Chanchal
Hi All, I want to create ffcharmm*.itp file from par_all36_carb.prm using the script provided by Mark Abraham. While I used execute the command ./ convert_charmm_to_gromacs.pl par_all36_carb.prm , I got this message: Argument "CTOFNB" isn't numeric in multiplication (*) at ./ convert_charmm_to_

Re: [gmx-users] error in converting charmm to gromacs

2009-11-20 Thread Justin A. Lemkul
Chanchal wrote: Hi All, I want to create ffcharmm*.itp file from par_all36_carb.prm using the script provided by Mark Abraham. While I used execute the command ./convert_charmm_to_gromacs.pl par_all36_carb.prm , I got this message: Argument "CTOFNB"

Re: [gmx-users] error in converting charmm to gromacs

2009-11-20 Thread Mark Abraham
Chanchal wrote: Hi All, I want to create ffcharmm*.itp file from par_all36_carb.prm using the script provided by Mark Abraham. While I used execute the command ./convert_charmm_to_gromacs.pl par_all36_carb.prm , I got this message: Argument "CTOFNB" is

[gmx-users] amber force field in gromacs

2009-11-20 Thread leila karami
Hi I used amber03 force field in gromacs to study pr-dna interaction. I compare my pdb file and ffamber03.rtp file. I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1) and C-terminal (NUMBER 70) of my protein is GLY. pdb file and rtp file relating to gly1 and gly70 are place

Re: [gmx-users] amber force field in gromacs

2009-11-20 Thread Mark Abraham
leila karami wrote: Hi I used amber03 force field in gromacs to study pr-dna interaction. I compare my pdb file and ffamber03.rtp file. I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1) and C-terminal (NUMBER 70) of my protein is GLY. pdb file and rtp file relating to