Re: [gmx-users] Error in equilibration

s lal badshah wrote: Dear Justin, I try again by correcting the typo mistake I made, this time it gives the following type of out put; You still have a bad starting structure, even after your EM. Have a look at these atoms that are causing the actual error messages, since it might be a local

[gmx-users] Error in equilibration

Dear Justin, I try again by correcting the typo mistake I made, this time it gives the following type of out put; Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 224.227448 (between atoms 1932 and 1934) rms 4.182895 bonds that rotated more than 30 degrees: atom

Re: [gmx-users] .itp file for polymer (Polystyrene)

Thanks Mark for guiding me. Mark Abraham <[EMAIL PROTECTED]> wrote: Rohit wrote: > Hi, > > I am trying to generate a polymer layer with 30 chains of 20 monomeric > units using gromacs' genbox command. For that, I need to have .itp file > for the single polymer chain (polystyrene). I have .itp f

[gmx-users] OPLS-AA/L

Check the archives. I posted a summary of one possible solution less than 8 hours ago. You will receive more assistance if you demonstrate that you are trying to help yourself. If you still don't find the answer that you are looking for then you need to be *way* more detailed in your questi

[gmx-users] System

Dear Justin, Hi, I want to do MD simulation of cholera toxin A-subunit.I took PDB file and remove other complexes from the protein so it comes to 185 amino acid residues.Through Whatif server I added the missing atoms. I uses oplsaa force field.Added about 11700 water molecules, closed it in cub

[gmx-users] OPLS-AA/L

Hi all, I am using gromacs 3.3.1 version.How can I generate OPLS-AA/L FF for POPC Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

Re: [gmx-users] Error in equilibration

s lal badshah wrote: Dear Justin & Mark, Hi! I made changes in my pr.mdp file but still the errors came.Please guide me. As you've read on the LINCS error page on the wiki, the errors are being caused by your starting structure being not-close-enough to something that makes physical sense, no

Re: [gmx-users] .itp file for polymer (Polystyrene)

Rohit wrote: Hi, I am trying to generate a polymer layer with 30 chains of 20 monomeric units using gromacs' genbox command. For that, I need to have .itp file for the single polymer chain (polystyrene). I have .itp file for styrene molecule, how can I make a .itp file for polymer chain using

Re: [gmx-users] Distance constrained energy minimization and MD

jayant james wrote: Hi all! The protein that I am trying to simulate has 3 chains. My aim is to apply harmonic constraints to certain parts of the protein and (based on FRET derived distances) I am attempting to incorporate distance constraint between certain amino acids of different chains

Re: [gmx-users] query about itp file of sugar

SHREYA RAY CHAUDHURI wrote: I wnt to generate an itp file for carbihydrate which contains a glucose,a galactose and a neuraminidase.I want to know which force fied to use and the the linkages to use for the sugar.Please let me know the way by which I can make the itp file for the sugar.Eagerly

[gmx-users] looking for help about the generating of opls forcefield

Hi all: How are you! I want to simulate the solution structure of a amino sugar gromacs, but I have no force field parameter about it. I have tried to obtain its forcefile parameter through prodrg and antechamber, and try my best to refine it. however, both calculated results with these forcef

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

maria goranovic wrote: An update: Using a 4th order PME spline resulted in ~ 15 % increase in efficiency. Thank you, Carsten. As you can see in some of the original PME papers, tweaking the parameters can give about an order of magnitude variation in the approximation error for given computa

[gmx-users] Distance constrained energy minimization and MD

Hi all! The protein that I am trying to simulate has 3 chains. My aim is to apply harmonic constraints to certain parts of the protein and (based on FRET derived distances) I am attempting to incorporate distance constraint between certain amino acids of different chains during EM and MD. *Harmon

[gmx-users] combining the OPLS-AA forcefield with the Berger lipids

To wrap up combination of the OPLS-AA forcefield with the Berger lipids, I have posted a detailed description of the motivation, method, and testing. Much of the methods there will be used in a paper at some point in time so please do not copy the text directly for your own use. http://www.pom

Re: [gmx-users] POL3 polarizable water model

Bo Zhou wrote: Dear Gromacs users, I wonder whether or not the POL3 polarizable water model (Caldwell JW, Kollman PA (1995) J Phys Chem 99: 6208-6219.) can be incorporated in gmx with amber03 force field. Thanks in advance. IIRC this is a point polarizability model. This is not implemented. The

Re: [gmx-users] POL3 polarizable water model

I believe the manual says that only the shell-on-a-spring model is supported by GROMACS for polarization. As far as I can recall, the POL3 model uses atomic multipoles, so tough luck for you... 2008/3/25, Bo Zhou <[EMAIL PROTECTED]>: > > Dear Gromacs users, > > I wonder whether or not the POL3 pol

[gmx-users] POL3 polarizable water model

Dear Gromacs users, I wonder whether or not the POL3 polarizable water model (Caldwell JW, Kollman PA (1995) J Phys Chem 99: 6208-6219.) can be incorporated in gmx with amber03 force field. Thanks in advance. Best regards ___ gmx-users mailing list

[gmx-users] Re: Informatin about Force field for Protein in POPC

Please keep this on the mailing list. I use OPLS + tip4p for protein in water, then I use the Berger lipids downloaded from Peter Tieleman's website using some special considerations for scaling of the 1-4 interactions. You can find some of my posts on that topic via searching for opls and ber

[gmx-users] Re: Hi

Please keep correspondence on the gmx-users listserv, so that an archived copy will be preserved for others to benefit from later. See my replies below. Quoting sudheer babu <[EMAIL PROTECTED]>: > Hi Mr. Justin, > Sorry for the posting my question to your personal mail, > You made me clear so m

[gmx-users] query about itp file of sugar

I wnt to generate an itp file for carbihydrate which contains a glucose,a galactose and a neuraminidase.I want to know which force fied to use and the the linkages to use for the sugar.Please let me know the way by which I can make the itp file for the sugar.Eagerly waiting for a reply,

Re: [gmx-users] Error in equilibration

> ewald_rtol = 1e5 I don't know if this is related or not, but ewald_rtol is, by default, 1e-5, so I suspect you've made a typo. > -- > step 0Warning: 1-4 interaction between 196 and 201 at distance 1.104 which

[gmx-users] .itp file for polymer (Polystyrene)

Hi, I am trying to generate a polymer layer with 30 chains of 20 monomeric units using gromacs' genbox command. For that, I need to have .itp file for the single polymer chain (polystyrene). I have .itp file for styrene molecule, how can I make a .itp file for polymer chain using .itp file of s

[gmx-users] error oxo

Dear experts, Hi! I see the following on the site: Error 0x0 and 0x1 From FaHWiki Jump to: navigation, search The 0x0 and 0x1 errors are unknown errors - all errors that are known will end with some other error code and message, but those errors that Pande Group hasn't

Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

An update: Using a 4th order PME spline resulted in ~ 15 % increase in efficiency. Thank you, Carsten. On Mon, Mar 24, 2008 at 3:08 PM, maria goranovic <[EMAIL PROTECTED]> wrote: > Dear All, > > My apologies. I had too big a simulation cell, and too few atoms, hence > the problem. > > No particu