[gmx-users] Fatal error during lipid bilayer minimization

2012-09-13 Thread Bharath K. Srikanth
Hi I am trying to simulate the self-assembly of course-grained DSPC lipids into a lipid bilayer. I made a box (7.5 x 7.5 x 7.5) containing 128 DSPC lipids, and added 768 molecules of water to the system, and ran a minimization (using em.mdp). The summary of the results is below. Reached the

Re: [gmx-users] LINCS warning in md run

2012-09-13 Thread Justin Lemkul
On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, this atom is the CG atom of the phosphate I added to the protein. But how can I find out by what it is punished? Visualization. This is the topology for this residue in the aminoacid.rtp file. I added it

Re: [gmx-users] Resuming of calculation from last *.cpt

2012-09-13 Thread Justin Lemkul
On 9/13/12 1:12 AM, James Starlight wrote: Dear Gromacs Users! I'm looking for possible way to resume trajectory calculations after that calculations have been stoped. Typically in such cases I start new task using cpt file from incomplete run. This produce new trajectory which start from

Re: [gmx-users] LINCS warning in md run

2012-09-13 Thread reisingere
Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md run. And there were no errors. And now I only added the phosphate to the

Re: [gmx-users] LINCS warning in md run

2012-09-13 Thread Justin Lemkul
On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Ah okey. Thank you. I will write them. Hmm, but the protein is a crystal structure from pdb with a resolution of 1.2. I already added the hydrogen atoms to this structure and there I already minimized them and made a md

[gmx-users] g_covar -reg

2012-09-13 Thread venkatesh s
Respected Sir / Madam i did temperature study for that i need analysis principal component analysis so, i followed GROMACS Introductory Tutorial (4.5.5) *g_covar* g_covar -s md_0_2.tpr -f md_merged_20_ns.xtc -o 2KW8_275_eigenval.xvg -v 2KW8_275_eigenvect.trr

Re: [gmx-users] Resuming of calculation from last *.cpt

2012-09-13 Thread James Starlight
Justin, I've used grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o incomplete.tpr mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append where incomplete.cpt was checkpoint from previous run and -o incomplete.tpr was the name for new trajectory (in that case its equal

Re: [gmx-users] Resuming of calculation from last *.cpt

2012-09-13 Thread Justin Lemkul
On 9/13/12 9:56 AM, James Starlight wrote: Justin, I've used grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o incomplete.tpr mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append where incomplete.cpt was checkpoint from previous run and -o incomplete.tpr was the

[gmx-users] Charmm for Proteins

2012-09-13 Thread Steven Neumann
Dear All, Could you please write me which is the latest version of Charmm force field for proteins? I want to study protein folding in explicit solvent. Is it available in Gromacs? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

Re: [gmx-users] Charmm for Proteins

2012-09-13 Thread Peter C. Lai
charmm27 is the canonical charmm protein FF, which is supported by gromacs. Note that if you are using gromacs prior to 4.5.5 to use -nochargegrp when using pdb2gmx when parameterizing your protein. On 2012-09-13 04:19:16PM +0100, Steven Neumann wrote: Dear All, Could you please write me

[gmx-users] Reg pdb2gmx for Cyclic peptide

2012-09-13 Thread vidhya sankar
Dear Justin Thank you for your Previous reply,    sorry for the inconvenience  to you personal Mail. I am doing MD  Cyclic Peptide  When I run  pdb2gmx , The Conect Infromation in pdb file are ignored . so that it is not

Re: [gmx-users] Reg pdb2gmx for Cyclic peptide

2012-09-13 Thread Justin Lemkul
On 9/13/12 11:42 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply, sorry for the inconvenience to you personal Mail. I am doing MD Cyclic Peptide When I run pdb2gmx , The Conect Infromation

[gmx-users] .xtc support in UCSF Chimera

2012-09-13 Thread Eric Pettersen
Thought people might want to know that thanks to the XTC Library, Chimera now support reading trajectories where the coordinates are in .xtc format. That support is only in the daily build of Chimera, not the production release. www.cgl.ucsf.edu/chimera --Eric Eric

[gmx-users] CfP: 3rd International Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim13) part of the Symposium on Theory of Modeling and Simulation SCS SpringSim 2013)

2012-09-13 Thread Daniele Gianni
# CALL FOR PAPERS 3rd International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS

[gmx-users] Segmentation fault (core dumped error)

2012-09-13 Thread Elie M
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that. (1) In an attempt to form the topology files of CNTs and graphene (using x2top),