Re: [gmx-users] g_sgangle---facing problem using this option

Richa taimni wrote: Dear all, while using the g_sangle option in gromacs to calculate the angle between 2 groups, and distance between 2 grps I m facing problem. As soon as I select the first grp frm the index file all the calculations are performed according to the first option..it does not ask

Re: [gmx-users] p4_error: interrupt SIGSEGV

Yangyang Shen wrote: Thanks for your reply, David. The mpich version, I think it is mpich-1.2.7 And I use gcc (is this one type of mpi lib?) to compile. Would pgi6.0 be another option? No PGI onky gives more trouble and less performance, see recent posts. Your best options are to install either

Re: [gmx-users] request

In God We Trust Hello Here is your topology. Thank you very much in advanceKarim MahnamInstitute of  Biochemistry  and  Biophysics (IBB)Tehran University P.O.box 13145-1384Tehran Iran http://www.ibb.ut.ac.ir/ -Original Message-From: hadi behzadi <[EMAIL PROTECTED]>To: gmx-users@groma

[gmx-users] g_sgangle---facing problem using this option

Dear all, while using the g_sangle option in gromacs to calculate the angle between 2 groups, and distance between 2 grps I m facing problem. As soon as I select the first grp frm the index file all the calculations are performed according to the first option..it does not ask me the second grp. Pl

RE: [gmx-users] PBC and large hydrogen-bonded molecules

Are you using VMD to view the trajectory? If so, in the Graphical Representations window, select the Periodic tab. Then get it to draw the periodic image to the right hand side of your "central / orginal" image. That will help with visualisation of what a PBC means and how it works. Catch ya, D

Re: [gmx-users] PBC and large hydrogen-bonded molecules

[EMAIL PROTECTED] wrote: Hello fellow Gromacs-users, Today I was extracting PDB snapshots from a solvated DNA 12mer simulation trajectory. When I went to view the snapshots, I saw that one of the DNA strands suddenly jumped some nanometers away from its partner during certain frames. I remembe

[gmx-users] PBC and large hydrogen-bonded molecules

Hello fellow Gromacs-users, Today I was extracting PDB snapshots from a solvated DNA 12mer simulation trajectory. When I went to view the snapshots, I saw that one of the DNA strands suddenly jumped some nanometers away from its partner during certain frames. I remembered that there was a note

Re: [gmx-users] p4_error: interrupt SIGSEGV

Thanks for your reply, David. The mpich version, I think it is mpich-1.2.7 And I use gcc (is this one type of mpi lib?) to compile. Would pgi6.0 be another option? Also I don't get this 'interrupt SIGSEGV' error for my other simulations. Do you have any clue why? Thanks a lot for your help. Yang

Re: [gmx-users] request

hadi behzadi wrote: hello I have a topology file for propanol as is in below , how we can obtain topology file for 100 molecule of propanol thanks chapter 5 are you sure you want this force field by the way? in the systems section write drg 100 ; ; ; This file was gen

[gmx-users] POPC simulation

Hi gmx-users,i am trying to run a POPC simulation. this is what i have done. i downloaded the popc128apdb, lipid.itp , popc.itp files from the following website http://moose.bio.ucalgary.ca/index.php?page=Downloads then i also downloaded the ffgmx_lipids files from the gromacs website.i have copie

[gmx-users] request

 hello I have a topology file for propanol  as is in below , how we can obtain topology file for 100 molecule of propanol thanks     ;   ;   ;   This file was generated by PRODRG version 051202.0518;   PRODRG written/copyrighted by Daan van Aalten;   ;   Questions/comm

[gmx-users] Parameters for unnatural amino acid F-Phe

Hi, I am trying to model a protein that contains 4-fluoro-phenylalanine. I've generated an entirely new set of parameters (using the Generalized Atom Force Field) to use in gromacs. I understand that I need to modify the .rtp file and aminoacid.dat files in order to obtain a .top file for t

Re: [gmx-users] p4_error: interrupt SIGSEGV

Yangyang Shen wrote: Hi, I get the following error immidiately after the mdrun starts p4_error: interrupt SIGSEGV: 11 It is also reproducible if I run the same simulation again. Could anyone please give me some hint? which mpich version? you probably need to recompile with another mpi lib.

[gmx-users] p4_error: interrupt SIGSEGV

Hi, I get the following error immidiately after the mdrun starts p4_error: interrupt SIGSEGV: 11 It is also reproducible if I run the same simulation again. Could anyone please give me some hint? Thanks a lot, Yangyang ___ gmx-users mailing list

Re: [gmx-users] Solventbox equilibration

Anthony Cruz wrote: Hi: I have been trying to made a solvent box of methacrylic acid using parameters from PRODRG. I change it to GROMOS96 parameters and use charges from DFT calculation. I do the energy minimization with out any problem. I run a 2ns MD (NVT) with out any problem too. But wh

[gmx-users] Solventbox equilibration

Hi: I have been trying to made a solvent box of methacrylic acid using parameters from PRODRG. I change it to GROMOS96 parameters and use charges from DFT calculation. I do the energy minimization with out any problem. I run a 2ns MD (NVT) with out any problem too. But when I try to run an MD

Re: [gmx-users] g_dist

Alan Dodd wrote: That'd certainly work if the movement is continuous, but if there are many fluctuations near the crossover point then sorting out which steps to fudge it at could be a pain. Assuming you only care about the Z seperation, I'd be tempted to use g_traj to plot both groups, and sub

Re: [gmx-users] g_dist

I can also use VMD - not quite as comfortable as g_dist with the pbc problem solved, but probably the quick and dirty 'fix', since I will have to look at the trajectories anyway. Thanks, Kay. On May 22, 2006, at 6:27 PM, Alan Dodd wrote: That'd certainly work if the movement is continuous,

[gmx-users] Re: g_dist

Hi Kay, How about using trjconv to remove periodicity ...then take the modified trajectory and feed it into g_dist? I think this could be a possible solution.. I'd appreciate it, if the hard working and ever resourceful users/developers can inform us whether this is a possible option??... i

Re: [gmx-users] g_dist

That'd certainly work if the movement is continuous, but if there are many fluctuations near the crossover point then sorting out which steps to fudge it at could be a pain. Assuming you only care about the Z seperation, I'd be tempted to use g_traj to plot both groups, and subtract the z-position

Re: [gmx-users] g_dist

yep, thanks! K. On May 22, 2006, at 6:15 PM, Xavier Periole wrote: Kay Gottschalk wrote: They are not interacting. The distance is larger than 40 Å. But still,if the distance to the mirror image is 41 Å and to the same protein in the box is 45 Å, the distance to the mirror image will b

Re: [gmx-users] g_dist

Kay Gottschalk wrote: They are not interacting. The distance is larger than 40 Å. But still,if the distance to the mirror image is 41 Å and to the same protein in the box is 45 Å, the distance to the mirror image will be plotted... We are indeed pulling on z. Best, Kay. Good, so the solu

Re: [gmx-users] g_dist

They are not interacting. The distance is larger than 40 Å. But still,if the distance to the mirror image is 41 Å and to the same protein in the box is 45 Å, the distance to the mirror image will be plotted... We are indeed pulling on z. Best, Kay. On May 22, 2006, at 6:02 PM, Xavier Periol

Re: [gmx-users] To add all hydrogens

[EMAIL PROTECTED] wrote: Dear All, First of all, I would like to give my thanks for the help David van der Spoel has given us. I'm doing an energy minimization with mdrun without problems. However, I've noticed that Gromacs is only adding the polar hydrogens and not all the hydrogens durin

Re: [gmx-users] g_dist

Kay Gottschalk wrote: Hi there, we are doing a pulling simulation and want to monitor the distance between two atoms during pulling. Using g_dist the distance is calculated between all mirror images of the periodic boundary conditions, and the minimal distance is calculated. In our case,

Re: [gmx-users] To add all hydrogens

Depends on the force field. Take opls/aa for all hydrogens.Best,Kay.On May 22, 2006, at 3:52 PM, <[EMAIL PROTECTED]> wrote:Dear All, First of all, I would like to give my thanks for the help David van der Spoel has given us. I'm doing an energy minimization with mdrun without problems. However, I

[gmx-users] To add all hydrogens

Dear All, First of all, I would like to give my thanks for the help David van der Spoel has given us. I'm doing an energy minimization with mdrun without problems. However, I've noticed that Gromacs is only adding the polar hydrogens and not all the hydrogens during the energy minimization. I wou

[gmx-users] g_dist

Hi there, we are doing a pulling simulation and want to monitor the distance between two atoms during pulling. Using g_dist the distance is calculated between all mirror images of the periodic boundary conditions, and the minimal distance is calculated. In our case, this is uncomfortable,

[gmx-users] Microcanonical

You should use neither, at least not for Coulomb. Only PME can be used for systems containing charges. For system containing exclusively neutral molecules, you can use a shift function, if the cut-off is longer than the range of the interaction. For water that would be roughly 1.2 nm. Be that

[gmx-users] Re: Dihedral around X,Y not found in topology.

After checking the tpr file with gmxdump I found all the 5 residues in the tpr file! So I really dont understand the source of the error.On 5/22/06, Abhishek Rathod <[EMAIL PROTECTED]> wrote: Hi,I am new to this list and to gromacs.I used a pdb file 1PLX from the PDB database and ran gromacs on it

[gmx-users] ions

Hi! I want to put in the box (with solvent) a lot of ions PO4--- How can I do it? I use genion, but the type PO4--- doesn't exist. I've the molecule created with Hyperchem. than you very much ___ Yahoo! Messenger with Voice: chiama da PC a telefo

[gmx-users] Dihedral around X,Y not found in topology.

Hi,I am new to this list and to gromacs.I used a pdb file 1PLX from the PDB database and ran gromacs on it.While running the g_rama function, I got the following error."Dihedral around 23,25 not found in topology. Using mult=3 Dihedral around 25,28 not found in topology. Using mult=3Dihedral around

Re: [gmx-users] Microcanonical

A B wrote: Please refer to my recent paper, J. Chem. Theor. Comp. 2 (2006) 1-11. Yes, this is exactly what I mean - an appropriate smoothing function ("shift") works fine, but simple group-based truncation does not; that this does not work has indeed been known since long before GROMACS was

[gmx-users] Microcanonical

Please refer to my recent paper, J. Chem. Theor. Comp. 2 (2006) 1-11. Yes, this is exactly what I mean - an appropriate smoothing function ("shift") works fine, but simple group-based truncation does not; that this does not work has indeed been known since long before GROMACS was born. Mayb

Re: [gmx-users] Microcanonical

can you please send this paper to me? email address : [EMAIL PROTECTED] regards, karamyog.On 5/22/06, David van der Spoel <[EMAIL PROTECTED]> wrote: A B wrote:> I am curious about the reason for the heating that allegedly occurs with> cutoffs in NVE simulations ("The use of (electrostatic) cutoff

Re: [gmx-users] Microcanonical

A B wrote: I am curious about the reason for the heating that allegedly occurs with cutoffs in NVE simulations ("The use of (electrostatic) cutoffs is well known to cause heating in NVE simulations."). This should not, and does not, happen if an appropriate smoothing function is applied. Does t

[gmx-users] Microcanonical

I am curious about the reason for the heating that allegedly occurs with cutoffs in NVE simulations ("The use of (electrostatic) cutoffs is well known to cause heating in NVE simulations."). This should not, and does not, happen if an appropriate smoothing function is applied. Does this heating

[gmx-users] parallel PME documentation request

Hi, While writing some scripts that iterated over PME parameters looking to satisfy some optimality criteria, I ran into a problem that grompp needs fourier_nx to be divisible by the number of nodes in order to construct the .tpr file. This isn't noted anywhere in the documentation, and it be