[gmx-users] PhD vacancy on MD modelling at University of Groningen

2013-09-12 Thread Patrick Onck
Dear all, A four-year computational Ph.D. position on "MD modelling of unfolded proteins in aging nuclear pores" is available at the University of Groningen, The Netherlands. For details, see http://imechanica.org/node/15081 For applications contact Prof.dr.ir. P.R. Onck at p.r.o...@rug.nl.

[gmx-users] Re: Umbrella sampling simulations using make_edi with -restrain and -harmonic

2013-09-12 Thread Poker Chen
I think you should add -tau 0 when using flooding as harmonic restraint (since you do not want the flooding potential to change). Okay, adding -tau 0 does turn it properly into a harmonic potential, according to edsam.xvg. However, the average position of the resulting (gaussian) is near but not

Re: [gmx-users] how to make a index file

2013-09-12 Thread Justin Lemkul
On 9/11/13 11:33 PM, aixintiankong wrote: i want to analyze the change of secondary structure of the mainchian frome residue 20 to residue 60. so i want to make a index file that only contain the maninchian+H from residue 20 to residue 60. i have inputed the command " make_ndx -f em.pdb -o ind

Re: [gmx-users] NMR restrained MD

2013-09-12 Thread Rama Krishna Koppisetti
Hi [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions be

Re: [gmx-users] NMR restrained MD

2013-09-12 Thread Justin Lemkul
On 9/12/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbo

[gmx-users] umbrella sampling using pull codes

2013-09-12 Thread mjyang
Dear GMX users, I'd like to perform the umbrella sampling using the pull codes in gromacs. The reaction coordinate is defined as the distance between the center of mass (DCOM) of two domains in a protein. The following script is used: --- only for pull section ; Pull code pull

Re: [gmx-users] umbrella sampling using pull codes

2013-09-12 Thread Justin Lemkul
On 9/12/13 9:55 AM, mjyang wrote: Dear GMX users, I'd like to perform the umbrella sampling using the pull codes in gromacs. The reaction coordinate is defined as the distance between the center of mass (DCOM) of two domains in a protein. The following script is used: ---

Re: [gmx-users] NMR restrained MD

2013-09-12 Thread Rama Krishna Koppisetti
Hi, These are the parameters I kept in the .rtp file for DMPC molecule. Still getting same error message should I need to look at somewhere else. [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate al

Re: [gmx-users] NMR restrained MD

2013-09-12 Thread Justin Lemkul
On 9/12/13 1:17 PM, Rama Krishna Koppisetti wrote: 1. Did you re-run pdb2gmx after modifying the .rtp file? Yes.. I do run with modified .rtp file but output was same as previous. 2. Have you looked into the [bonds] directive in the .top file that pdb2gmx created to see if anything is out of

Re: [gmx-users] NMR restrained MD

2013-09-12 Thread Rama Krishna Koppisetti
1. Did you re-run pdb2gmx after modifying the .rtp file? Yes.. I do run with modified .rtp file but output was same as previous. 2. Have you looked into the [bonds] directive in the .top file that pdb2gmx created to see if anything is out of place? Every line should have 5 entries: [bonds] dire

Re: [gmx-users] NMR restrained MD

2013-09-12 Thread Justin Lemkul
On 9/12/13 2:57 PM, Rama Krishna Koppisetti wrote: Hi Justin, Output topology from pdb2gmx. You could see some entries differ between two molecules. I'm looking forward to do restrained MD for this system by using Gromacs. [ moleculetype ] ; Namenrexcl Protein 3 [ at

Re: [gmx-users] NMR restrained MD

2013-09-12 Thread Rama Krishna Koppisetti
Hi Justin, Output topology from pdb2gmx. You could see some entries differ between two molecules. I'm looking forward to do restrained MD for this system by using Gromacs. [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr

Re: [gmx-users] NMR restrained MD

2013-09-12 Thread Justin Lemkul
On 9/12/13 11:03 AM, Rama Krishna Koppisetti wrote: Hi, These are the parameters I kept in the .rtp file for DMPC molecule. Still getting same error message should I need to look at somewhere else. [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals

[gmx-users] RE: average pressure of a system

2013-09-12 Thread Dwey Kauffman
>> I carried out independent NPT processes with different tau_p values = > >> 1.5, >> 1.0 and 0.5 >> >> >> >> ## tau_p 1.5 >> Energy Average Err.Est. RMSD Tot-Drift >> --- >> >> Pressure

Re: [gmx-users] changing atom types versus adding dihedrals to atom types

2013-09-12 Thread Rafael I. Silverman y de la Vega
I see, when you say thorough parametrization and validation, what do you mean? How does one validate the system, calculate free energy in solution and compare it to tabulated data? On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul wrote: > > > On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega

RE: [gmx-users] umbrella sampling using pull codes

2013-09-12 Thread mjyang
Dear Justin, Thanks for your reply. I checked the content in pullx.xvg file as follows: # GRowing Old MAkes el Chrono Sweat # @title "Pull COM" @xaxis label "Time (ps)" @yaxis label "Position (nm)" @TYPE xy @ view 0.15, 0.15, 0

Re: [gmx-users] RE: average pressure of a system

2013-09-12 Thread Justin Lemkul
On 9/12/13 6:37 PM, Dwey Kauffman wrote: I carried out independent NPT processes with different tau_p values = 1.5, 1.0 and 0.5 ## tau_p 1.5 Energy Average Err.Est. RMSD Tot-Drift --- ---

Re: [gmx-users] changing atom types versus adding dihedrals to atom types

2013-09-12 Thread Justin Lemkul
On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote: I see, when you say thorough parametrization and validation, what do you mean? How does one validate the system, calculate free energy in solution and compare it to tabulated data? The target data depend on the force field for whi

Re: [gmx-users] umbrella sampling using pull codes

2013-09-12 Thread Justin Lemkul
On 9/12/13 10:18 PM, mjyang wrote: Dear Justin, Thanks for your reply. I checked the content in pullx.xvg file as follows: # GRowing Old MAkes el Chrono Sweat # @title "Pull COM" @xaxis label "Time (ps)" @yaxis label "Posit

RE: [gmx-users] umbrella sampling using pull codes

2013-09-12 Thread mjyang
Dear Justin, What is the meaning of the "minus number" for the distance in the 3rd column? Does it mean that the moving group is at the minus direction wrt the reference group along Z? Many thanks. Mingjun From: gmx-users-boun...@gromacs.org [gmx-u

Re: [gmx-users] umbrella sampling using pull codes

2013-09-12 Thread Justin Lemkul
On 9/12/13 10:41 PM, mjyang wrote: Dear Justin, What is the meaning of the "minus number" for the distance in the 3rd column? Does it mean that the moving group is at the minus direction wrt the reference group along Z? Yes, since it is a vector quantity. The positions should be very