[gmx-users] rmsd between different monomers

Dear all I made an index file with 4 different groups for 4 different chains (since my protein is a tetramer) and then run g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out to get the rmsd between two different monomers from the same structure, it asked me two different groups and I gave 0

Re: [gmx-users] Generating topology with pdb2gmx

Moeed wrote: Dear Justin, 1- Unfortunately, I am having difficulty running the simple program pdb2gmx with pdb file you sent me for Hexane.. I have in working directory pdb file and rtp files: Hexane-PRODRG.pdb rtp.pdb pdb2gmx -f Hexane-PRODRG.pdb -o Hexane.gro -p Hexane.top >& output.pd

[gmx-users] Generating topology with pdb2gmx

Dear Justin, 1- Unfortunately, I am having difficulty running the simple program pdb2gmx with pdb file you sent me for Hexane.. I have in working directory pdb file and rtp files: Hexane-PRODRG.pdb rtp.pdb pdb2gmx -f Hexane-PRODRG.pdb -o Hexane.gro -p Hexane.top >& output.pdb2gmx output.pdb2gmx

Re: [gmx-users] gromacs doubt

On 8/05/2010 8:40 PM, manjula kasinathan wrote: hi all i'm doing simulation for complex structure (protein length around 1020). while running mdrun for position restrain it shows error like this Step 434, time 0.868 (ps) LINCS WARNING See http://www.gromacs.org/index.php?title=Docu

Re: [gmx-users] Force constant for position restraints

On 8/05/2010 8:30 PM, shahab shariati wrote: Hi gromacs users there is a option in pdb2gmx command : -posrefc (Force constant for position restraints). and also there is following lines in top file: #ifdef POSRES #include "posre.itp" #endif which of them is better way for position restraint simul

[gmx-users] gromacs doubt

hi all i'm doing simulation for complex structure (protein length around 1020). while running mdrun for position restrain it shows error like this Step 434, time 0.868 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1818.708939, max 108974.859375 (between atoms 1917 and

[gmx-users] Force constant for position restraints

Hi gromacs users there is a option in pdb2gmx command : -posrefc (Force constant for position restraints). and also there is following lines in top file: #ifdef POSRES #include "posre.itp" #endif which of them is better way for position restraint simulation and determining of force constant? Any

Re: [gmx-users] PCA component

Hi, Of course you can filter along one eigenvector. My guess is that the option for 3d projection was also selected (-3d)... Cheers, Tsjerk On May 8, 2010 10:08 AM, "David van der Spoel" wrote: On 2010-05-08 08.45, Anirban Ghosh wrote: > > Hi ALL, > > I am trying to do a PCA for my simulatio

[gmx-users] Re: configure error

> On 7/05/2010 11:59 PM, Emily Curtis wrote: > > Hi Lina, > > > > Did you ever figure out why you were getting the message: > > > > gromacs checking size of void*... configure: error: cannot compute > > sizeof (void*) > > > > I am also getting this error. I have read the configure.log a million > >

Re: [gmx-users] gromacs

On 8/05/2010 6:29 PM, manjula kasinathan wrote: hi all i'm doing Md simulation in gromacs while running the mdrun for position restrain it shows error like this " segmentation fault". can anyone help me y this error occurs and how to come across it. thank in advance. We can't help you if

[gmx-users] gromacs

hi all i'm doing Md simulation in gromacs while running the mdrun for position restrain it shows error like this " segmentation fault". can anyone help me y this error occurs and how to come across it. thank in advance. -- With Regards, Manjulakasinathan -- gmx-users mailing listgmx-us

Re: [gmx-users] PCA component

On 2010-05-08 08.45, Anirban Ghosh wrote: Hi ALL, I am trying to do a PCA for my simulation. I generated a covarience matrix using g_covar and now I want to visualize the motion only along first principal component. So with g_anaeig I gave the option "-first 1" "-last 1". But it gave the error a