Re: [gmx-users] (no subject)

Bio wrote: Dear gmxns, HOpe u r enjoying the simulation. I have one trouble while executing a position restraint simulation to equilibrate for 100 ps for a protein ,it takes more time..I come to know that it is good if it takes not more than a day...Eventhough I strictly followed the procedur

[gmx-users] (no subject)

Dear gmxns, HOpe u r enjoying the simulation. I have one trouble while executing a position restraint simulation to equilibrate for 100 ps for a protein ,it takes more time..I come to know that it is good if it takes not more than a day...Eventhough I strictly followed the procedure,the PR simu

[gmx-users] gromacs local pressure version

Hello users, I am trying to calculate local pressure, and I found local pressure version of gromacs-3.0 in user contrubution. It's great enough, but gromacs 3.0 version had been modeified to support the local presure calculation, and also it does not support pme for coulomb interaction. So, I a

Re: [gmx-users] pulling force

Giacomo Bastianelli wrote: Dear Users, I would like to use a force that during the dynamics will bring closer my two molecules. Is there any way to implement this function? Section 6.2 of the manual. Mark ___ gmx-users mailing listgmx-users@grom

Re: [gmx-users] request

hadi behzadi wrote: Program grompp, VERSION 3.3 Source code file: topio.c, line: 385 Fatal error: Invalid order for directive moleculetype, file ""1.top"", line 17 The line 17 is [ moleculetype ]. As it says, this directive is out of order. You have to #include some forcefield files first, whi

RE: [gmx-users] request

>Fatal error: >Invalid order for directive moleculetype, file ""1.top"", line 17 >The line 17 is [ moleculetype ]. >I request you all to give suggestion for this. Go to www.gromacs.org, click on the link that says search, which will take you to http://www.gromacs.org/external/search.html In the

[gmx-users] Re:request

t;", line 17 > The line 17 is [ moleculetype ]. > > > I request you all to give suggestion for this. > > > > I will be very thankful to you. > > > > > > > > - > Any questions? G

[gmx-users] pulling force

Dear Users, I would like to use a force that during the dynamics will bring closer my two molecules. Is there any way to implement this function? Thanks in advance, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gro

[gmx-users] request

Hi all users I constructed topology and gro (1.gro and 1.top) file for propane ( CH3CH2CH3) molecule from PRODRG server as follow: 1.go PRODRG COORDS 3 1DRG CAB 1 -0.128 0.172 0.000 1DRG CAA 2 -0.128 0.019 0.000 1DRG CAC 3 0.01

[gmx-users] Re: Segmentation falt error - installing gromacs-3.3.1 on Mac-OSX

Hi David, Yes, I did source $GMXBIN/GMXRC or GMXRC.csh (for my tcsh) to setup the environment. This did not solve the problem. thanks, Ibrahim At 04:26 AM 12/2/2006, you wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via th

[gmx-users] ATP/ADP topology for OPLS

Hello gmxlers, I am searching OPLS topologies files for ADP or ATP. Unfortunately I found only ADP / ATP topologies for amber94/99 G53a5/a6 or older forcefields; however I would prefer to use the OPLS forcefield. Does anyone have an ADP.itp file for OPLS? Or alternatively does someone have

[gmx-users] COM motion removal after simulation

Hi all, Is it possible to remove the COM movement of a protein after the simulation? i tried it with trjconv but couldn't make it work: trjconv -f traj.xtc -pbc cluster -s topol.tpr -n index.ndx -o trajout.xtc -center rect I select "Protein" for clustering and centering and "System" for output