[gmx-users] Remove my email

Please remove my email. -- 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to

[gmx-users] Problem with continuation of files using checkpoint files

? Thanks in advance. Regards Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests

Re: [gmx-users] eigenvalues

. Is this really related to the difference in the degrees of freedom of two different systems (that I am a bit skeptic about) with which you are confusing it now. If I am missing something here, then anyone please correct me. Regards, Monika On Thu, Jan 8, 2009 at 4:31 PM, sanja...@iitb.ac.in wrote

Re: [gmx-users] eigenvalues

Hi Tsjerk, Thank you very much for correcting me. And yes that is variance, not the literal motion. Regards, Monika On Fri, Jan 9, 2009 at 6:50 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Monika, As far as I know, PCA analysis breaks your total motion in system, or rather decouples

[gmx-users] RMSD calculations by g_rms

the things are going hay-ward?? For g_rms, I am using backbone for least square fit and protein for rmsd calculation. Similar pattern in all. Any kind of suggestions are welcome.. Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Dimer simulations using Gromacs

is that is it normal for gromacs to read dimer as single unit in .gro file. Or do I need to make some modifications in .gro and .top file to make it read as two entities. Suggestions are required for this. Thanking you, Regards, Monika ___ gmx-users

[gmx-users] REMD using Gromacs 3.2.1

? Is replica exchange can be done using 3.2.1? If yes, then how to perform REMD? (I mean the commands) Thanks in advance. Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] karthik

there and do accordingly. Gromacs installation is quite straightforward. Happy Installing!!! Monika On Wed, 2007-12-19 at 12:02 +0530, Anupam Nath Jha wrote: hii i am karthik while installing gromacs in linux redhat entriprise version i encountered problems like fftw3 3.0.1,and libfftw3f.so.3

[gmx-users] Temperature range for Gromacs (OPLS)

are temperature dependent, so till what temperature will the usage be fine for the default parameters with OPLS force field. Thanking you in advance, Regards, Monika. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: [gmx-users] Temperature range for Gromacs (OPLS)

Hello!! I have asked this question since I want to do simulation at 480K to look for high-temperature behavior. Will it be correct if I simulate at this temperature?? Thanking you, Regards, Monika David van der Spoel wrote: Monika wrote: Dear All, I wish to know that at what temperature

Re: [gmx-users] Temperature range for Gromacs (OPLS)

. But I will try to remain in the limit to avoid generating scrapped results. Thanking you, Regards, Monika Xavier Periole wrote: On Mon, 17 Dec 2007 16:12:28 +0530 Monika [EMAIL PROTECTED] wrote: Hello!! I have asked this question since I want to do simulation at 480K to look for high

Re: [gmx-users] Replica Exchange MD using Gromacs

Thank you very much all for your consideration and fruitful advices. Regards, Monika On Wed, 2007-12-05 at 18:15 +1100, Mark Abraham wrote: Xavier Periole wrote: Dear Monika, the setup of a REMD simulation is actually quite straightforward. In the following I describe steps

Re: [gmx-users] Replica Exchange MD using Gromacs

of advice from the experts who have successfully implemented REMD using Gromacs. Thanks a lot.. Regards, Monika On Fri, 2007-11-30 at 14:27 +0200, OZGE ENGIN wrote: Hi Monica, I had not found a detailed tutorial about it; however, you can search for papers in which the simulations are performed

[gmx-users] Replica Exchange MD using Gromacs

and the right protocol to do so.. Thanks a lot in advance.. Regards, Monika CCNSB, IIIT, Hyderabad. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] Nucleic Acid Simulations with Gromacs

guide me through?? Thanks in advance Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

Re: [gmx-users] Nucleic Acid Simulations with Gromacs

Thank you all for helping me. I will surely try the ffamber ports available. Regards, monika Yang Ye wrote: Please don't use the OPLS NA forcefield. It is largely based on AMBER (OPLS takes different approach in parameterization, so you know that direct migration is so correct

Re: [gmx-users] Storage of large output files

and efficient way to store their data. Regards, Monika Mark Abraham wrote: Monika Sharma wrote: Dear All, We have started our venture into MD recently, for which we are using our in-house resources. Now that MD runs are giving very large output files like for trr files. The files keep piling up and using

Re: [gmx-users] Another problem with Stimulated Annealing

. Please do suggest... regards, Monika David van der Spoel wrote: Monika Sharma wrote: Dear All, While doing SA, I am observing that when i am using steep as option for minimization, then the md log file generated takes ref_t as 0K temp only, but when i am using md as integratore, the temp for ref_t

Re: [gmx-users] grompp or parameter file problem?

water molecules also? Do check their representation also... Cheers.. Monika Yang Ye wrote: On 6/21/2007 6:20 PM, Anna Reymer wrote: On 6/20/07, Mark Abraham [EMAIL PROTECTED] wrote: Anna Reymer wrote: Hello all! I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port. I

Re: [gmx-users] grompp or parameter file problem?

Hello Anna, One thing. It is that the topology file includes in solvent topology section is tip3p.itp, but you are using amber99. Is it same as ffamber_tip3p.itp. If not, then i think you can try changing it to ffamber_tip3p.itp.. Hope it helps.. Monika Yang Ye wrote: On 6/21/2007 6:20 PM

[gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem

a dummy, and cannot execute. I even tried using as make CFLAGS='-mcpu=power5 -mtune=power5' for fftw and gromacs also, but it doesnt seems to work. If anyone can please help me out to osrt this problem.. Thanks in advance Monika ___ gmx-users mailing list

Re: [gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem

I am using Gromacs3.3 version, and I was trying grompp for energy minimization, which is not working. Even the mdrun didnt work. The same file seems to work properly on simple Fedora linux PC, but not on IBM Power linux. Dont know then what the problem is?? Mark Abraham wrote: Monika Sharma