Re: [gmx-users] How can i know if the protein swell during the MD simulation?

How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar > Hi, > > Well, I think 'swelling' is unambiguously, though roughly, defined as > 'growing larger', which suggests that you'd have to look for an > increase in volume. But how to do that, how to define the volume of > the protei

[gmx-users] Failing installation with --enable-mpi option

I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix="_mpi" it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix="_mpi" checki

Re: [gmx-users] Failing installation with --enable-mpi option

Thanks Justin, will try your suggestion.. 2009/5/20 Justin A. Lemkul : > > > Bhanu wrote: >> >> I tried to install Gromacs on my Core2Quad pc with the command >> >>  ./configure --enable-mpi --disable-nice --program-suffix="_mpi" >> >>

Re: [gmx-users] Failing installation with --enable-mpi option

Dear Justin, could you please write what environmental changes you made to MPICC.. I tried to alter the profile, but it is rejecting all of them.. Bhanu. On 20/05/2009, Bhanu wrote: > Thanks Justin, will try your suggestion.. > > 2009/5/20 Justin A. Lemkul : > > > > > &g

[gmx-users] Strange error in DNA simulations..

ption -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -deffnm string bhanu Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc.) i

Re: [gmx-users] Strange error in DNA simulations..

On 15/06/2009, Mark Abraham wrote: > > > On 06/15/09, *Bhanu * wrote: > > Hi Group, > I've tried simulating a five bp dna. It has showed many atoms missing and > some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and > -mising options. Later editc

Re: [gmx-users] Strange error in DNA simulations..

Hi, I didn't ignore your link, I was trying all things suggested in wiki.. Its the greed for more and more suggestions made me to type those.. Anyway, thanks for the link, buddy! On 15/06/2009, Mark Abraham wrote: > > > > On 06/15/09, *Bhanu * wrote: > > > > On 15

Re: [gmx-users] problem in dna-protein simulation

Edit your pdb as per ur rtp file / forcefield. On 16/06/2009, Justin A. Lemkul wrote: > > > > nitu sharma wrote: > >> Dear all, >> >>i am trying to simulation of dna-protein complex using >> gromacs with amber port . I am using amber99 port with gromacs-4.0.3 >> version. I am

[gmx-users] Protein is moving out of box.

Hi all, am new to Gromacs. I tried a 10 ps simulation with a protein and after the run, the protein came out of the box.. is it good or bad? How can I keep the protein in the box? Waiting for ur reply. Bhanu. -- _ _ (_)(_) (,,) =()= ((__)\ _|L\___/ The Lab Rats

Re: [gmx-users] protein/dmso simulation

Try "genbox -cp *.gro -ci dmso.gro -p *.top -o *.gro" Gro file for dmso comes built-in with gromacs 3.3. As Justin has directed, forcefields do matter. On 19/08/2008, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > prasun kumar wrote: > >> dear users >> I am trying to run the simulation fo a

[gmx-users] Genion failing in parallel runs.

Hi, I'm using Gromacs 3.3.3, installed with double precision. When I run genion with this command: genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral the following error message was generated: Program g

[gmx-users] DSSP and g_sas

Which among DSSP and g_sas is better for calculating solvent accessible surface area of proteins? -- Bhanu Prakash. -- 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

Re: [gmx-users] DSSP and g_sas

Using DSSP we can also calcuate the surface area, though it doesn't allow changes in probe diameter etc. it does calculate the surface area. I just wish to know whether the performance of DSSP is comparable to g_sas? Should it be used? -- Bhanu Prakash, BARC. > Shalom Bhanu, &