Re: [gmx-users] Problems with calculating Cv and Cp

> > Hi Andrew Paluch, > You had asked me to supply the formulas that I attempted using to calculate Cv. The formula from J. M. Haile is labelled isometric heat capacity and given by Cv = Nk/(N-NT*(3(N/2)-1)) and the one in Allen and Tildesley is quite complicated to write out (has some speci

[gmx-users] Analyzing Protein-Ligand Interactions

Hello All, I am trying to analyze the output of repeated molecular docking runs, so that I further refine the protein-ligand complex using GROMACS, and determine the free energy of the system. Is there a program that can process a number of ligand structure files (output of docking runs) as input

Re: [gmx-users] low concentration simulation ?

Chih-Ying Lin wrote: Hi From Justin, "If you say that you have 20 mM of ligand, which corresponds to 18 ligands attached to one protein, why not just put 18 molecules in your unit cell with one protein? " => I want to save the simulaiton time since i will run the simulation up to 1 mic

[gmx-users] low concentration simulation ?

Hi >From Justin, "If you say that you have 20 mM of ligand, which corresponds to 18 ligands attached to one protein, why not just put 18 molecules in your unit cell with one protein? " => I want to save the simulaiton time since i will run the simulation up to 1 micro-sencond. => 18 ligand + one

Re: [gmx-users] define a new covalent bond in gromacs

Hans HEINDL wrote: mdrun-openmm does not yet support any restraints But gromacs does. Therefore, it seems you need to patch openmm, for which you probably want to contact the openmm team. Hans Am Dienstag, den 05.01.2010, 22:12 +0100 schrieb David van der Spoel: Hans HEINDL wrote: Hi all,

Re: [gmx-users] Incomplete frame,while running trjconv .....

pavan payghan wrote: HI i have to create .xtc file to save my disk space,but while i was running it using trjconv i got warning message "incomplete frame".Actually i was running my system on four nodes with mdrun_mpi but it stopped due to unavailability of disk space so from this

[gmx-users] low concentration simulation ?

Mark already answered this: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047825.html --original message -- HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands att

Re: [gmx-users] low concentration simulation ?

Chih-Ying Lin wrote: HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands attached on one protein) It will be a huge system to create a system with 20 mM and it will take lo

Re: [gmx-users] Error during minimization

nishap.pa...@utoronto.ca wrote: I have a question regarding the simulations that I am running. I tried creating a pdb file with one methane and water molecules, but the system keeps showing 'bad contact' error when I run the minimization step and I don't understand what I am doing wrong. Thi

[gmx-users] low concentration simulation ?

HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands attached on one protein) It will be a huge system to create a system with 20 mM and it will take lot of simulation time. Inste

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

Thanks a lot the ultrafast response ! Arik Justin A. Lemkul wrote: Arik Cohen wrote: Dear Gromacs users, In continuation to the problem below, it seems that self interaction is not the problem since a -d 1.5nm around the protein should have been more than enough. Not noticing earlier, I s

Re: [gmx-users] define a new covalent bond in gromacs

mdrun-openmm does not yet support any restraints Hans Am Dienstag, den 05.01.2010, 22:12 +0100 schrieb David van der Spoel: > Hans HEINDL wrote: > > Hi all, > > > > I need to restrain the distance of two atoms in my system (the distance > > is around 57 angstroms). As we plan to use mdrun-openm

Re: [gmx-users] define a new covalent bond in gromacs

Hans HEINDL wrote: Hi all, I need to restrain the distance of two atoms in my system (the distance is around 57 angstroms). As we plan to use mdrun-openmm which presently does not support neither distance nor position restraints we need to create a new covalent bond between the two atoms which

Re: [gmx-users] define a new covalent bond in gromacs

Hans HEINDL wrote: Hi all, I need to restrain the distance of two atoms in my system (the distance is around 57 angstroms). As we plan to use mdrun-openmm which presently does not support neither distance nor position restraints we need to create a new covalent bond between the two atoms which w

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

Arik Cohen wrote: Dear Gromacs users, In continuation to the problem below, it seems that self interaction is not the problem since a -d 1.5nm around the protein should have been more than enough. Not noticing earlier, I see strange files being created with the name "step1150b_n1.pdb" (a bu

[gmx-users] define a new covalent bond in gromacs

Hi all, I need to restrain the distance of two atoms in my system (the distance is around 57 angstroms). As we plan to use mdrun-openmm which presently does not support neither distance nor position restraints we need to create a new covalent bond between the two atoms which would restrain the dis

Re: [Fwd: Re: [gmx-users] A problem with a "detaching Calpha/s"]

Dear Gromacs users, In continuation to the problem below, it seems that self interaction is not the problem since a -d 1.5nm around the protein should have been more than enough. Not noticing earlier, I see strange files being created with the name "step1150b_n1.pdb" (a bug like structural rep

[gmx-users] Helpful Information Energy Minimization errors

Hello gmx users, After running energy minimization steps, I got the following error: teepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps= 100 Step=0, Dmax= 1.0e-02 nm, Epot= -2.84750e+04 Fmax= 1.53401e+04, atom= 2501 Step=1, Dmax= 1.0e-02 nm, E

[gmx-users] Error during minimization

Hi Nisha, you say "And it runs minimization with bad contact errors", but I don't see any indication of that error message here. Is it perhaps that your EM exits early and then your MD throws an error? In any event, please post complete error information as output by gromacs. Chris. -- origi

Re: [gmx-users] grompp segmentation error

ram bio wrote: Dear Justin, Thanks for the response. Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers. $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s = Linux u

[gmx-users] Incomplete frame,while running trjconv .....

Your disk was full and the .xtc file could not be completely written, therefore you have an incomplete frame. I think that you have answered your own question here. If I was you, I would trjconv -e to get the full trajectory minus the last incomplete frame for a good .xtc file. There are ot

[gmx-users] implement brenner potential

Hello, Do you know there is any way to implement Brenner potential to GROAMACS? Thank you,Kasim _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go

[gmx-users] Incomplete frame,while running trjconv .....

HI i have to create .xtc file to save my disk space,but while i was running it using trjconv i got warning message "incomplete frame".Actually i was running my system on four nodes with mdrun_mpi but it stopped due to unavailability of disk space so from this it is certain that my syst

[gmx-users] Error during minimization

I have a question regarding the simulations that I am running. I tried creating a pdb file with one methane and water molecules, but the system keeps showing 'bad contact' error when I run the minimization step and I don't understand what I am doing wrong. This is my methane file : TITLE

[gmx-users] angle_restraints_z and -ddcheck

I have determined that the proper solution here is to use particle decomposition. -noddcheck simply delays the inevetable fatal LINCS error. Nevertheless, mdrun -pd requires that one maintains whole molecules in the starting conformation: http://lists.gromacs.org/pipermail/gmx-users/2010-Ja

Re: [gmx-users] grompp segmentation error

Dear Justin, Thanks for the response. Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers. $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s = Linux uname -v = #1 SMP Mo

[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

Thanks Berk, I actually did not have continuation = yes. I still use old-style .mdp options unconstrainted_start and gen_vel (see below), although these get replaced by grompp. Quoting grompp: "Replacing old mdp entry 'unconstrained_start' by 'continuation'" gpc-f101n084-$ grep continuation

RE: [gmx-users] 10-4-3 implicit wall potential

Hi, Why not use the tabulated wall potential? That does not require are changes to the code. Berk > Date: Tue, 5 Jan 2010 14:13:30 +0100 > From: qia...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-users] 10-4-3 implicit wall potential > > HI all, > > Does anyone have experience to im

[gmx-users] 10-4-3 implicit wall potential

HI all, Does anyone have experience to implement the 10-4-3 implicit wall potential? If I want to use it, which files do I need to change, except wall.c? Can anyone give some suggestions? Thanks a lot! best wishes, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

Re: [gmx-users] How to modify the initial CG reduction structure to the usable one matching the .itp atom designation?

Aymeric Naômé wrote: Dear users, By what mean does one correct te CG structure file generated with the atom2cg script to the final structure matching the .itp file atom types? I mean, how to convert the PDB-like format with generic atom types (BN0, SC1, SC2, SC3) of atom2cg output file to th

[gmx-users] How to modify the initial CG reduction structure to the usable one matching the .itp atom designation?

Dear users, By what mean does one correct te CG structure file generated with the atom2cg script to the final structure matching the .itp file atom types? I mean, how to convert the PDB-like format with generic atom types (BN0, SC1, SC2, SC3) of atom2cg output file to the proper .gro structure

RE: [gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

Hi, This should not be a requirement. I have not tested this, but from the code it seems this problem can only occur when you have the mdp option continuation turned on. Berk > Date: Sun, 3 Jan 2010 15:53:36 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-user

[gmx-users] order parameter for unsaturated chains

Hi, I want to obtain order parameter for unsaturated carbons (eg. 9, 10) on oleoyl (18 carbons) chains. i use -Scd= 2/3 Sxx +1/3 Syy for the saturated carbons. I try to calculate order parameters for unsaturated carbons, which is defined as: Scd=1/4Szz + 3/4 Syy + sdr(3)/2 Syz , with ignore thi

Re: [gmx-users] Fwd: What could be wrong with rdf plot?

Yes of course but I was not sure g_rdf allowed it! The solutions are actually explained in the g_rdf -h ... On Jan 4, 2010, at 10:06 PM, Dallas B. Warren wrote: Wouldn't it be simpler to just exclude the intramolecular -OHs when you actually generate the RDF? Catch ya, Dr Dallas Warren Ph

Re: [gmx-users] Wrong bond and Lennard-Jones potentials in cyclohexane

Henri Ervasti wrote: Dear all, Thank you for your help and comments on abovementioned problem. In the end though it turned out that the large potentials were caused by overlapping rings (two rings were going through inside each other) which genbox unfortunately somehow had generated. I hadn't th

[gmx-users] Wrong bond and Lennard-Jones potentials in cyclohexane

Dear all, Thank you for your help and comments on abovementioned problem. In the end though it turned out that the large potentials were caused by overlapping rings (two rings were going through inside each other) which genbox unfortunately somehow had generated. I hadn't though of that myself unt

Re: [gmx-users] united atom and coarse grained

leila karami wrote: Hi what is difference between united atom and coarse grained force fields? Please start with a Google search. For example, Wikipedia has useful content on this topic. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

[gmx-users] united atom and coarse grained

Hi what is difference between united atom and coarse grained force fields? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please do

Re: [gmx-users] N and C terminal in proteins

leila karami wrote: Hi in md simulation of protein, when N-terminal and C-terminal should be NH2 and COOH and when NH3+ and COO- respectively? When one or other seems to make biochemical sense in the context of the system being modelled. At neutral pH, peptides tend to be zwitterionic. Ma

[gmx-users] N and C terminal in proteins

Hi in md simulation of protein, when N-terminal and C-terminal should be NH2 and COOH and when NH3+ and COO- respectively? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://