[gmx-users] REgarding redefined error.

Dear all gromacs users, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: moleculetype CU1 is redefined Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-us

[gmx-users] Reg trr file

Hello all, I am doing protein-ligand dynamics using GROMACS. i could get all the final files after simulation like gro,edr, log files. But i couldnt get the trr file.Can anyone of you please tell me wht should i do to get this or tell me at what step i have done this mistake. Thank you -- *Ramya

Re: [gmx-users] intermolecular H bond selection

On Mon, May 21, 2012 at 3:09 AM, mu xiaojia wrote: > Thanks for prompt answering but I may need to clarify my question and > sorry for the understanding, > > For example, I have dipeptides like Ala-Ala, how to ask g_hbond only > calculate the h bonds between Ala on different dipeptides instead of

[gmx-users] LIE methodology check (mdrun -rerun cutoffs and box vectors)

Greetings all, Background: I have a series of MD runs of a protein ligand complex where I have used PME, they represent far more calculations than I have time to repeat in full. I recently became aware that the coulombic interaction energy reported when PME is used is not valid for use with g_l

[gmx-users] characterising monolayer molecule rotation

Greetings Gromacs, Long time reader, first time poster. I am modelling monolayer/water systems composed of long-chain fatty alcohols and have observed the molecules to rotate around their long-axis, I would like to characterise this using GROMACS. I have had some success calculating the rotational

Re: [gmx-users] restart REMD

try put -s before -deffnm mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski wrote: > Hi Francesco, > > Thanks! > However, it does not work with my case.. > > tomek > > On Sun, May 20, 2012 at 1:47 PM, francesco oteri < > francesco

Re: [gmx-users] restart REMD

Hi Francesco, Thanks! However, it does not work with my case.. tomek On Sun, May 20, 2012 at 1:47 PM, francesco oteri wrote: > Hi, > usually I use something like: > > mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* > * > * > gromacs is smart enough to understand that it has to load

Re: [gmx-users] intermolecular H bond selection

Thanks for prompt answering but I may need to clarify my question and sorry for the understanding, For example, I have dipeptides like Ala-Ala, how to ask g_hbond only calculate the h bonds between Ala on different dipeptides instead of counting all the possible h bonds between Ala(intermolecularl

[gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

Dear gromacs users, does someone of you know whether parameters for the detergent dodecyl-beta-maltoside are avalaible in MARTINI forcefield? Thank you in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the ar

Re: [gmx-users] constraints between protein ligand - metal chelation

Hi, if you are able to define atom couples able to mantein the structure of your complex, you can insert in .top file a set of bond using function 6 (see table at pag 125 of the user manual). For example, let atom 1 and 100 are at distance 0.6nm, you can insert in .top a row like 1 100 6 0.6 1000

Re: [gmx-users] What is the autocorrelation time

Dear Chris, As I see it there one can interpret the acf and correlatation time further for certain types of data. I'll use the h-bond autocorrelation function as an example. Here the data is time series of logical true and false, represented as ones and zeros. This type of acf can be direcly in

Re: [gmx-users] restart REMD

Hi, usually I use something like: mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* * * gromacs is smart enough to understand that it has to load topol_1.cpt topol_2.cpt ecc.ecc Anyway, you can do a small test, i.e. using 5 replicas and stopping you simulation after a few seconds

[gmx-users] restart REMD

Hi, I am running REMD simulation: mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000 I am getting files with name like -s* (for example -s1.trr) How now I could restart this simulation? I know that for regular MD simulation only I need -cpi cpt_file_name --append to add, but what with REMD s

[gmx-users] parameters of a residue

Dear gmx users, Corresponding to your suggestions, I get the parameters for new defined residues from SwissParam. The parameters are not accurate completely. May I face any problem when getting the PMF? and specially for publishing a paper for this reason that the parameters are not accurate as