[gmx-users] using gromacs for peptpoids

hello all   can we use gromacs G43A1 or ggmx ff for simulations of peptoids   regards nur -- 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 don't post (un)subscri

[gmx-users] Comparing different conformations of a polypeptide

Dear All   I have run different conformations of a polypeptide in spc water for 1ns, keeping the box size, volume and no. of water molecules same. Can i compare the enrgies of the different conformations after simulation and on its basis say which one of them is stable. also, to see the

[gmx-users] problem using makehole program

Dear All i started makehole program...but am facing problems setting the mdp parameters. when i gave mdrun command i get an error..that i cant make out: the command i gave is:- /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun -v -hole -holep hpgr.mdp -s dmpc_water_1ns.tpr -o cecmel311334_dmpc_hol

[gmx-users] Problems using makehole program

Dear All i started makehole program...but am facing problems setting the mdp parameters. when i gave mdrun command i get an error..that i cant make out: the command i gave is:- /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun -v -hole -holep hpgr.mdp -s dmpc_water_1ns.tpr -o cecmel311334_dmpc_

[gmx-users] how to restraint peptide bond

Dear all I want to put restraint on peptide bond and analyse in both cis and trans form. But hor to put these restraints?? regards nur - Did you know? You can CHAT without downloading messenger. Click here__

[gmx-users] Problem in starting make hole

Sir i want to use makehole program (gromacs 3.1.4)and i used the grompp command on dmpc.pdb with position restraints as specified in the tutorial. the position restraint file is as follows : [ position_restraints ] ; atom type fx fy fz 8 1 0.0 0.0 1000.0

[gmx-users] problem using makehole grompp

Sir I installed the makehole program as given in instructions, by making a separate copy of gromacs and then added the makehole tar file to it. Then followed the normal steps for installation. But when i set the mdp file as given in tutorial and try to give the grompp command, it does no

[gmx-users] Starting a simulation of a peptide

Dear I am really thankfull to tsjerk and Mark for making me understand the defaults. I v removed the defaults section from the lipid.itp as it aws also ther in ffgmx.itp.. but now it gives an error "Atomtype CA not found!" regards nur --

[gmx-users] To Tsjerk "Starting a simulation of a peptide lipid bilayer"

Dear Sir I have checked the links you gave and also checked my files ...the ffgmx.itp has not been included several times the lipid.itp file has a line [default] 11 [atomtypes] ... What does the 1 1 under the default section imply... and i st

[gmx-users] Starting a simulation of a peptide lipid bilayer

Dear all I am sorry...but i tried all suggestions to start the run of the lipid bilayre...but failed. i looked into the mailing list and found some options. one of the mail said to remove the 1 from the [defaults] 1 1, column in the lipid.itp, but as i do say it gives an error sa

[gmx-users] starting a simulation of a peptide lipid bilayer

Dear All I got the lipid topology files from http://moose.bio.ucalgary.ca/. and it also gives the lipid.itp file. When i include both the lipid and my required dppc.itp file in the topology file...it gives an error saying;"Invalid order for directive atomtypes, file "lipid.itp", line 9...wh

[gmx-users] starting a peptide bilayer simulation run

Dear all I want to study my peptide in a bilayer system and so for this i got the structure and topology for the lipid bilayer from the site moose.bio.ucalgary.ca I want to study the orientation and interactions of the peptide with the outer surface of the membrane, do gain insight about ho

[gmx-users] Simulation in octanol as solvent

Dear All I have added octanolas solvent...but now my problem is that if i take the itp file as available on the gromacs site (which is in ffoplsaa) there are too many warnings related to bond types and if i get an itp generated through prodrg then it excludes the aliphatic hydrogens, while my g

[gmx-users] Simulation in octanol as solvent

Dear All.. i want to add octanol as solvent...bt everytime i give genbox command it says 0 solvent molecules added. I got the octanol equilibrated box from gromacs contributors section. it was of ffooplsa type...when i changed the atom types and topology through prodrg...the same problem persi

[gmx-users] Simulation in octanol as solvent

Dear All I want to study a peptoid sequence in octanol as solvent Please guide me how to proceed. I got the octanol eqilibrated box topology files from GROMACS site, (gromacs users contributors section)..but am not able to add my peptoid sequence to it...moreover the octanol box model that i g

[gmx-users] Fwd: Position Restraint time for octanol

Dear All When simulating in a box of octanol, what should be the optimal position restraint run time. Regards nur - Here’s a new way to find what you're looking for - Yahoo! Answers -

[gmx-users] Parameter file for AFM pulling

Dear ALL Can anyone provide me a simple protocol to start AFM pulling on lipid bilayer to study mambrane-protien simulations. Also, how to make a *.mdp file for it. regards nur - Here’s a new way to find what you're looking

[gmx-users] How to set the dielectric constant

Dear All, Can any one let me know how to change the dielectric constant. Regards Nur - Here’s a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing list

[gmx-users] How to do simmulated annealing

Dear All, Can any one give me a simple protocol to start with simmulated annealing. Regards Nur - Here’s a new way to find what you're looking for - Yahoo! Answers ___ gmx-users ma

[gmx-users] How to do simmulated annealing

Dear All, Can any one give me a simple protocol to start with simmulated annealing. Regards Nur - Here’s a new way to find what you're looking for - Yahoo! Answers ___ gmx-users ma

[gmx-users] How To Adjust the Ionizataion State

Dear All Please let me know how to adjust the ionization state of the amino acid side chains and what is the default pH taken in Molecular Dynamics. regards nur - Here’s a new way to find what you're looking for - Yahoo! An

[gmx-users] Placing the molecule in the centre of the box

Dear All I set up my molecule in the centre of the box using editconf command and -c option. Then i solvate the box and run the md step. But after the Simulation the molecule doesnot remain anywhere near the centre. Please suggest Regrads nur Send free SMS to your Friends on Mobile f

[gmx-users] pdb for a structure with more then 300 atoms

Dear all I have a peptoid sequence (peptoids have the amino acid side chain appended to the amide nitrogen rather then alpha carbon) with more then 300 atoms. Please guide me an easy way to generate its pdb or gromacs coordinate and topology files, as PRODRG server doesnt work for more then 300

[gmx-users] Pressure variation in NPT ensemble

Dear all I set the pressure in NPT ensemble to 1bar..and run the simulation. But, the log file does not show the same pressure...for some cases it does remain close to 1 but in others it even shows around 4 bars of pressure. What is the significance of this variation...and what should i do

[gmx-users] Simulation of two peptides

Dear all When we simulate two or more peptides/structures together, does gromacs select the best possible orientations of the structures. Regards nur - Find out what India is talking about on - Yahoo! Answers India Sen

[gmx-users] thannks Mark

Dear Mark Thanks a lot for your gidance. Regards nur - Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW___

[gmx-users] To Mark: cg in vaccum

Dear Mark Thanks for your guidance. But I am not clear with what you wrote regarding my question: is their any particular value of emtol in mdp files of steep and cg, that we should use... I use emtol=1000 in the steep file, and then when i do cg i keep it 100, 50, 10, 8, 2 step by step. Pleas

[gmx-users] Simulation in vaccum

Dear ALL when we simulate in vaccum, first we do steepest descent, then conj, then md in vac. I want to know that, Do we use periodic boundary conditions here..and also if we dont specify anything about pbc in mdp file wht does gromacs take it as... Also please tell me, is their any parti

[gmx-users] energy minimisation in vaccum

dear all When we do energy minimisation in vaccum...what ensemble should we use... nur - Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8.

[gmx-users] how to simulate at a specific dielectric constant

Dear all How can i set the dielectric constant of my choice in the simulations regards nur Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW___

[gmx-users] error after mdrun

Dear All I am new to gromacs...please help me and let me know how to proceed..when i give the mdrun command he terminal displays the following: /usr/local/gromacs/bin/mdrun -nice 0 -v -s hyb2b_vac_md.tpr -o hyb2b_vac_md_1ns_traj.trr -c hyb2b_vac_md_1ns.gro -e hyb2b_vac_md_1ns_ener.edr -g hyb2b_vac

[gmx-users] error says "segnentation fault"

Dear All everytime i give the command mdrun...the terminal stops after some steps and says segmentation fault regards nur Find out what India is talking about on - Yahoo! Answers India Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW

[gmx-users] Problem in setting rlist, rcoulomb

When I set the  *.mdp file as follows:  ; Steepest escent in vacuo ; hyb2a ; ; Input File ; cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 500 ; ; Energy minimising stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid morse = no coulombtype = Shift vdw_type = Shift rlis

[gmx-users] Problem interprating the results

I am new to gromacs and need help regarding interpratation of the results...where to look for[EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.orgTo subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-usersor, via em

[gmx-users] how to start simulation of a peptide in bilayer

I am new to gromacs and need guidance to start a simulation of a peptide in bilayer. Please guide [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.orgTo subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-usersor,