[gmx-users] rmsd between different monomers

Dear all How can we calculate the rmsd between different monomers from of a protein. for example I have a tetramer and I have to calculate the rmsd between chain A to B, A to C and A to D with time. I was trying using g_rms but couldn't do that. thanks with regards anupam -- Science is facts

Re: [gmx-users] rmsd between different monomers

There is one web-server in our lab. http://10.188.1.15/3dss/ Use third option. On Fri, May 7, 2010 at 2:41 PM, Anupam Nath Jha wrote: > > Dear all > > How can we calculate the rmsd between different monomers from of a protein. > for > example I have a tetramer and I have to calculate the rmsd bet

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: Yes， I load my coarse-grained PDB ,then load ps as data, but the stucture still was full of points . Is a proper "!NBOND" section generated in your .psf file? If the script finishes without any errors, the output should be viable. -Justin -- ===

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

Yes, the PSF file has NBOND section and the script finished without any errors! But it does not show any bonded! Thank you！ --- 10年5月7日，周五, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Gromacs Us

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

xi zhao wrote: Yes, the PSF file has NBOND section and the script finished without any errors! But it does not show any bonded! Thank you！ Can you send me your coordinate file and .psf file (off-list) so I can see if there's anything to diagnose? If you have an NBOND section, the script

[gmx-users] PCA component

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 as:

Re: [gmx-users] rmsd between different monomers

On 7/05/2010 7:11 PM, Anupam Nath Jha wrote: Dear all How can we calculate the rmsd between different monomers from of a protein. for example I have a tetramer and I have to calculate the rmsd between chain A to B, A to C and A to D with time. I was trying using g_rms but couldn't do that. g

[gmx-users] domain decomposition

Hello! I am new to Gromacs and especially at parallel runs. I have some problem running my system using domain decomposition. I apologize but it will be a long mail... My system is made up by a membrane protein embedded is a mixed lipid bilayer (POPE/POPG). I tried to run it on 8 nodes but the si

Re: [gmx-users] domain decomposition

Hi Try with -dd 2 x 2 x 2 option with 8 nodes and check the performance. I too got the same problems, i could overcome with symmetrical -dd option. Srinivas. On Fri, May 7, 2010 at 8:57 AM, irene farabella < i.farabe...@mail.cryst.bbk.ac.uk> wrote: > Hello! > > I am new to Gromacs and especiall

[gmx-users] configure error

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 times and I still can't figure out why I am getting this message. The stran

Re: [gmx-users] error in hydrocarbon dihedrals of opls-aa?

On 5/7/10 8:45 AM, Markus Tusch wrote: Hi everybody, I've just compared the following opls-aa torsional parameters for hydrocarbons given in J. Comp. Chem., Vol. 18, No. 16, 1955 - 1970 (1997) as well as in J. Comp. Chem., Vol. 23, No. 15, 1416 - 1429 (2002) with those in ffoplsaabon.itp (Gromac

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

I discovered the problem. There was a case of pattern matching that wasn't working, so an extra bond was being written between atom 0 and atom 0, which of course is nonsense. Also be advised that the .psf file was mangled anyway, since you had tried to process different topologies (that did

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

It well done! thank you very much! zhao --- 10年5月7日，周五, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Gromacs Users' List" 日期: 2010年5月7日,周五,下午10:15 I discovered the problem.  There was a case o

Re: [gmx-users] 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 times and I still can't figure o

RE: [gmx-users] make_edi, g_covar -nofit

Hi Carsten, I downloaded the clone and patches, copied make_edi.c to /src/tools and recompiled gromacs-4.0.7 as suggested by Mark. Now make_edi works with .trr files generated using either g_covar -nofit or -fit but the .edi files generated now have only the average structure recorded under both

[gmx-users] PCA component

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 as: