Re: [gmx-users] citation for pdb2gmx -vsite hydrogens

That's the one. 7 maj 2012 kl. 22.34 skrev Christopher Neale: Dear users: I am writing my methods section for a simulation in which I used -vsites hydrogens and I want to ensure that I have the reference correct. The gmx-4.5.4 manual does not list a reference that I could see for this

[gmx-users] Re: Justin lipid-position restraine

On Tue, May 8, 2012 at 1:00 PM, rama david ramadavidgr...@gmail.com wrote: Hi Gromacs user, I am doing the justin tutorial on lipid posted on link.. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I am following the tutorial very carefully

Re: [gmx-users] Getting local pressure

g_density 8 maj 2012 kl. 03.29 skrev cuong nguyen: Dear, Could anyone please let me know, in Gromacs analysis is there any way to get the local pressure (along z-axis of the box)? Thanks a lot! Cuong Nguyen -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: Justin lipid-position restraine

On Tue, May 8, 2012 at 1:01 PM, rama david ramadavidgr...@gmail.com wrote: On Tue, May 8, 2012 at 1:00 PM, rama david ramadavidgr...@gmail.comwrote: Hi Gromacs user, I am doing the justin tutorial on lipid posted on link..

Re: [gmx-users] Calculation of the components of (ionic) current using g_current

Hi, it is the ionic current, given by a sum over the center of mass velocities of each molecule by their net-charge. /Flo On Mon, 2012-05-07 at 13:00 -0400, Andrew DeYoung wrote: Hi, g_current calculates the (ionic) current in the output file specified by the -o switch (by default,

[gmx-users] justin-lipid tutorial........

Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii of carbon from the 0.15 to 0.375 Is

Re: [gmx-users] justin-lipid tutorial........

On 5/8/12 8:06 AM, rama david wrote: Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hello, I assume that you mean pull_pbcatom0... Nothing changes when I set this to an atom index I am afraid. I saw that you had use pull_geometry=cylinder in your recent JACS paper. Would it be too much to ask to see those pull settings? I simply cannot get the molecule to stay at the desired

[gmx-users] Formyl parameters

Dear gmx users, My .pdb input file has a formyl group which is not defined in CHARMM27 and CHARMM36. So I  got its .itp file through swissparam. Now I want to use its parametrs. As I read in gromacs.org ,  I need to include this .itp in .top file. How does it come when I have not got any .top

Re: [gmx-users] Formyl parameters

On 5/8/12 11:25 AM, Shima Arasteh wrote: Dear gmx users, My .pdb input file has a formyl group which is not defined in CHARMM27 and CHARMM36. So I got its .itp file through swissparam. Now I want to use its parametrs. As I read in gromacs.org , I need to include this .itp in .top file. How

[gmx-users] restarting simulation after segmentation fault

Dear gmx users I am simulating a system involving carbon nanotube. I successfully completed the EM,NVT and NPT equilibration phase and then started to run production  simulation(NVT ensemble) for 10 ns.However, after passing more than 50 steps(1 ns),I gave the segmentation error.I

Re: [gmx-users] restarting simulation after segmentation fault

On 5/8/12 11:40 AM, Za Pour wrote: Dear gmx users I am simulating a system involving carbon nanotube. I successfully completed the EM,NVT and NPT equilibration phase and then started to run production simulation(NVT ensemble) for 10 ns.However, after passing more than 50 steps(1 ns),I gave

[gmx-users] radius of gyration

Dear GROMACS Specialists, I have one question about radius of gyration for micelle, Please help me. My micelle is created at 10 ps by Martini CG force field. When I calculate the radius of gyration from this time as g_gyrate -f 1.xtc -s 1.tpr -n 1.ndx -o gyrate.xvg -b 10 and g_analyze -f

Re: [gmx-users] radius of gyration

On 5/8/12 1:06 PM, dina dusti wrote: Dear GROMACS Specialists, I have one question about radius of gyration for micelle, Please help me. My micelle is created at 10 ps by Martini CG force field. Does this mean that during the first 100 ns, there is no micelle? That is, it is only

[gmx-users] Wild-card atomt types - regd

Dear Gromacs users, I am planing to use wildcard atomtypes in [ dihedrals ] directive of the ffbonded.itp file, As my system contain O-C dihedral, all the O-C dihedrals are same, so instead of mentioning each dihedral explicitly i have tried wildcard atom types by

Re: [gmx-users] Wild-card atomt types - regd

On 5/8/12 1:44 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to use wildcard atomtypes in [ dihedrals ] directive of the ffbonded.itp file, As my system contain O-C dihedral, all the O-C dihedrals are same, so instead of mentioning each dihedral

[gmx-users] (no subject)

Dear Justin I really appreciate for your reply. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the

[gmx-users] Charge derrivation for OPLSAA forcefield

Hi Guys I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP based charges for some molecules that I study. Is this a correct method to do so if not please let me know what are the other methods that are available. thanks alot   Milinda Samaraweera University of

[gmx-users] (no subject)

Hi Guys I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP based charges for some molecules that I study using OPLSAA force field. Is this a correct method to do so if not please let me know what are the other methods that are available. thanks alot   Milinda

[gmx-users] Slow-growth method question

Hello community, I recently ran several simulations using the g_bar method on several molecule decouplings and I even applied it to some functional group mutations and it seems to work out quite well so far. The only thing is that it requires several simulations to run. I'm attempting to

[gmx-users] radius of gyration

Dear Justin, Thank you very much from your help. Yes, the micelle was created after 100 ns from start of simulation. If the first procedure is true, so why the error estimate is so small and why the error estimate of Rg is so different with Rg(x,y,z)? Please help me. Best Regards Dina --

Re: [gmx-users] radius of gyration

On 5/8/12 4:08 PM, dina dusti wrote: Dear Justin, Thank you very much from your help. Yes, the micelle was created after 100 ns from start of simulation. If the first procedure is true, so why the error estimate is so small and why the error estimate of Rg is so different with Rg(x,y,z)?

[gmx-users] radius of gyration

Dear Justin, Thank you very much from your help, but may I ask you to say me why the error estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand any thing from paper about this problem! Best Regards Dina From: Justin A. Lemkul

Re: [gmx-users] radius of gyration

On 5/8/12 4:50 PM, dina dusti wrote: Dear Justin, Thank you very much from your help, but may I ask you to say me why the error estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand any thing from paper about this problem! The value of Rg is calculated from the

Re: [gmx-users] Formyl parameters

Where does swissparam get its parameters for charmm? and does it use custom atomtypes for generic molecules? I have been using CGenFF-derived parameters for molecules that aren't in base c36 and I think it's working well for me... -- Sent from my Android phone with K-9 Mail. Please excuse my

[gmx-users] system cooling down when runing NVE

Dear Gromacs experts, I'm just a newbaby in Gromacs, and hence I have a lot of problem when running this program. I try to run NVE simulation of a protein. First, I run an NTP ensemble, follow by NVT and finally, NVE. In NPT and NVT, T remains as constant, however, in NVE simulation,

Re: [gmx-users] system cooling down when runing NVE

you have position restraints on, which I expect would damp collisions between solvent and solute. temp drops towards some sort of equilibrium, which doesn't necessarily match your starting temp even though energy of the system is conserved ..sounds like expected behavior to me? -- Sent from my

[gmx-users] radius of gyration

Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 9, 2012 4:52 AM Subject: Re:

Re: [gmx-users] Formyl parameters

What do you mean? Am I supposed to use CGenFF to derive parameters? Cheers, Shima From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 9, 2012 5:20 AM Subject: Re: [gmx-users] Formyl parameters

[gmx-users] Re: Fwd: HEME-cysteine gromacs simulation

Zhang Bing, I guess it is problem in your visualizers. Try to label the atom using VMD which goes well with most of the file types derived in GROMACS. I hope you'll see the atom as FE not just F. Thanks Peterson -- View this message in context: