Re: [gmx-users] more digits

Shuangxing Dai wrote: Hi, all, I need more digits to input information. But the default format of pdb file for coordinate is %8.3f. Can I modify the pdbio.c file to achive this goal? Or is there any other direct ways to input more digits coordinate information in Gromacs? Use a g96 file.

[gmx-users] g_energy => RMSD vs Fluctuation

Hi The definition of the Fluctuation is shown on the Manual, Appendix C, eqn (C.1) The definition of the RMSD is as shown from the link. http://en.wikipedia.org/wiki/Root_mean_square_deviation The definition of the estimators is unclear though. So, what is the definition of the estimators? The fo

Re: [gmx-users] Re: x2top (David van der Spoel)

danilo gonzalez wrote: mr spoel, i have the .top for my system using PRODRG, but when I try run this .top with the next command editconf -bt cubic –f DRGFIN.gro –o poli12.pdb –d 0.9, the program gives me the next error message __- Program editco

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Chih-Ying Lin wrote: Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 0. Do more background reading. :-) 1. From Berk => use multiple groups. => how ??? => I have been thinking that it is better to group the molecule => such a

[gmx-users] Re: x2top (David van der Spoel)

mr spoel, i have the .top for my system using PRODRG, but when I try run this .top with the next command editconf -bt cubic –f DRGFIN.gro –o poli12.pdb –d 0.9, the program gives me the next error message __- Program editconf, VERSION 3.3.3 Source co

[gmx-users] The Cut-off for coulombtype heat up the water system?

/Personal/justin > > > ___ > 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 b

Re: [gmx-users] more digits

Shuangxing Dai wrote: > Hi, all, >I need more digits to input information. But the default format of > pdb file for coordinate is %8.3f. Can I modify the pdbio.c file to > achive this goal? Or is there any other direct ways to input more digits > coordinate information in Gromacs? Use a .g9

[gmx-users] trjconv -pbc atom -center rect

Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. with this command => trjconv -pbc atom -center rect the most part of the protein is still in the right edge of the box the small par

Re: [gmx-users] trjconv -pbc -center

Hi, I answered a very similar question last week but it appears that gmx-users is not online by now: try to use this script. And be aware to re-wrap code lines as my mail splits it. Please comment if it actually works for you. Best. Daniel *** Usage notes: - Just copy/and/paste the code

Re: [gmx-users] trjconv -pbc -center

Chih-Ying Lin wrote: Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I supposed that the ligands dock/attach on the protein. I want to center the protein and see if the ligands

[gmx-users] trjconv -pbc -center

Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I supposed that the ligands dock/attach on the protein. I want to center the protein and see if the ligands dock/attach on the protei

Re: [gmx-users] g_energy => RMSD = Standard Deviation?

Chih-Ying Lin wrote: HI After the command g_energy => the value of RMSD is shown, I can not find the math definition of RMSD from manual. Is the math definition of RMSD = Standard Deviation in Statistics? First Google result for "root mean square deviation": http://en.wikipedia.org/wiki/R

[gmx-users] g_energy => RMSD = Standard Deviation?

HI After the command g_energy => the value of RMSD is shown, I can not find the math definition of RMSD from manual. Is the math definition of RMSD = Standard Deviation in Statistics? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] coulombtype = Reaction-Field => heat up the system

Hi I set up Tcoupl = Berendsen. ref_t = 300 K the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? the final Temp = 303 K and stable. Can I analyze the data from this simulation? The simulation

[gmx-users] g_energy => both instantaneous and average

Hi I have read throught the Appendix C. The following is the .mdp file. Type the command g_energy -f abc-NVT500.edr -o abc-NVT500.xvg choose Pressure Based on my understanding of the Appendix C => g_energy will print out the instantaneous Pressure every 1000 step and save it into abc-NVT500.xv

Re: [gmx-users] Final Temp = 303 K ?

Chih-Ying Lin wrote: Hi Here is my whole md.mdp. But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? Yes, and I explained why. Specify options yourself, don't rely on defaults! -Justin

[gmx-users] Final Temp = 303 K ?

Hi Here is my whole md.mdp. But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? The simulation system is protein + ligand + counter ions. ligand is the 33-atom molecule. force field ffG45a3.

[gmx-users] more digits

Hi, all, I need more digits to input information. But the default format of pdb file for coordinate is %8.3f. Can I modify the pdbio.c file to achive this goal? Or is there any other direct ways to input more digits coordinate information in Gromacs? Thanks in advance. Shuangxing Dai_

Re: [gmx-users] mpi mdrun

jayant james wrote: Hi! After installing GMX without the mpi Igive the following commands make clean ./configure --enable-mpi --disable-nice --program-suffix="_mpi" I am getting this problem when I give the --enable-mpi option checking size of int... configure: error: cannot compute sizeo

Re: [gmx-users] g_energy

Chih-Ying Lin wrote: Hi I have read the manual , Appendix C. After the command g_energy => Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -196428372

[gmx-users] g_energy

Hi I have read the manual , Appendix C. After the command g_energy => Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -196428372.215340.8525.1803

Re: [gmx-users] Final Temp = 303 K ?

Chih-Ying Lin wrote: Hi I was running the MD simulation and you the Berendsen method. Here is my .mdp file. ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 30

Re: [gmx-users] mpi mdrun

Hi! After installing GMX without the mpi Igive the following commands make clean ./configure --enable-mpi --disable-nice --program-suffix="_mpi" I am getting this problem when I give the --enable-mpi option checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64

[gmx-users] Final Temp = 303 K ?

Hi I was running the MD simulation and you the Berendsen method. Here is my .mdp file. ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 But the final Temp =

Re: [gmx-users] g_order and the tpr file

age.skje...@biomed.uib.no wrote: Dear GROMACS users, I've simulated a membrane system with AMBER 9.0, and now I'm trying to calculate order parameters for the carbon atoms in the fatty acid tails with the help of g_order. I've converted my AMBER trajectory to gromacs xtc and gro files. How

[gmx-users] g_order and the tpr file

Dear GROMACS users, I've simulated a membrane system with AMBER 9.0, and now I'm trying to calculate order parameters for the carbon atoms in the fatty acid tails with the help of g_order. I've converted my AMBER trajectory to gromacs xtc and gro files. How can I obtain the tpr file neede

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Dear Justin: Thank you so much for your answer. That helps a lot! On Thu, Jun 18, 2009 at 10:35 AM, Justin A. Lemkul wrote: > > > Yanmei Song wrote: > >> Dear Justin: >> >> Thanks for your response. >> >> The reason I am doing this is that I wanted to test what the different >> electrostatics t

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? That is one

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Yanmei Song wrote: Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17,

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Dear Justin: Thanks for your response. The reason I am doing this is that I wanted to test what the different electrostatics treatments will affect my results. So the heating up is normal by using a plain cut-off and the results can not be trusted, right? On Wed, Jun 17, 2009 at 5:20 PM, Justin

Re: [gmx-users] Re: Re: protein in SDS/water

Anna Marabotti wrote: Dear Justin, AAARRRGGGHH! The last case indicated in the wiki section about 0 topology was MY case: probably I was using a .mdp file that was created with Windows. When I re-wrote my em.mdp file using vi, it worked!! I'm sorry for all this waste of time, but as I told som

Re: [gmx-users] mpi mdrun

jayant james wrote: Hi! Thanks for your reply. So I suppose I need to have a hostfile in my directory and call it during the mpirun command. I have one clarification, since I am using a quad core how am I to list the processors on the host file? would it need to open a file name \d hostfile

Re: [gmx-users] mpi mdrun

On Thu, 2009-06-18 at 10:03 -0700, jayant james wrote: > Hi! > Thanks for your reply. So I suppose I need to have a hostfile in my > directory and call it during the mpirun command. I have one > clarification, since I am using a quad core how am I to list the > processors on the host file? would i

Re: [gmx-users] mpi mdrun

Hi! Thanks for your reply. So I suppose I need to have a hostfile in my directory and call it during the mpirun command. I have one clarification, since I am using a quad core how am I to list the processors on the host file? would it need to open a file name \d hostfile and have a list for exampl

Re: [gmx-users] make install 'only suffix append binaries'

Dear Mark, Thank you very much for your reply. Indeed, reading more about Fink I can see several alternative. For now I guess I got a good solution. I have a package called 'gromacs-all' which installs gromacs single and double and now I want to make too with mpi, but first I need to solve a prob

[gmx-users] Re: Re: protein in SDS/water

Dear Justin, AAARRRGGGHH! The last case indicated in the wiki section about 0 topology was MY case: probably I was using a .mdp file that was created with Windows. When I re-wrote my em.mdp file using vi, it worked!! I'm sorry for all this waste of time, but as I told some days ago, I've proble

Re: [gmx-users] make install 'only suffix append binaries'

Alan wrote: Hi List, I would like to know if there's an option in gromacs Makefile that would allow me to once did: ./configure --disable-float --program-suffix="_d" --enable-shared make Then install only the binaries created with suffix "_d". I am not sure if 'make install-exec' would do it

[gmx-users] make install 'only suffix append binaries'

Hi List, I would like to know if there's an option in gromacs Makefile that would allow me to once did: ./configure --disable-float --program-suffix="_d" --enable-shared make Then install only the binaries created with suffix "_d". I am not sure if 'make install-exec' would do it or if there's

Re: [gmx-users] problem in grompp -broken charge

Samik Bhattacharya wrote: hi, Justin, i have completed upto the genion step of that simulation. One error is creeping in this step which is nonzero system charge. my system is said to have a charge 1.69. now how to neutralize this kind of broken charge? another thing is that how this kind of b

[gmx-users] problem in grompp -broken charge

hi, Justin, i have completed upto the genion step of that simulation. One error is creeping in this step which is nonzero system charge. my system is said to have a charge 1.69. now how to neutralize this kind of broken charge? another thing is that how this kind of broken chage is being develop

Re: [gmx-users] Parallel computation in Gromacs 3.2.1 Reg.

chandran karunakaran wrote: Dear Gromacs users We are interested in doing long time MD using parallel computation.Can we use the Gromacs 3.2.1 version in the parallel computation system. We would appreciate if you suggest what type of parallel computing system to be bought to implement in Groma

Re: [gmx-users] Re: How to obtain the .gro and .top files for dendrimers

wuxiao wrote: > Dear gmx users, > In order to get more direct help, some words need to be added to the > question for the first time. That's a good idea. > The dendrimer I want to study is just PAMAM, ethylenediamine (EDA) > cored and amine surface poly(amidoamine). The pdb file for the PAM

[gmx-users] Parallel computation in Gromacs 3.2.1 Reg.

Dear Gromacs users We are interested in doing long time MD using parallel computation.Can we use the Gromacs 3.2.1 version in the parallel computation system. We would appreciate if you suggest what type of parallel computing system to be bought to implement  in Gromacs. Thank you Dr C.Karunaka

[gmx-users] Re: How to obtain the .gro and .top files for dendrimers

Dear gmx users, In order to get more direct help, some words need to be added to the question for the first time. The dendrimer I want to study is just PAMAM, ethylenediamine (EDA) cored and amine surface poly(amidoamine). The pdb file for the PAMAM has assumed to be obtained, and I want

Re: [gmx-users] How to obtain the .gro and .top files for dendrimers

wuxiao wrote: > Dear gmx users, > On current, I plan to study a dendrimer (like PAMAM) using MD > simulations available in GROMACS. As is well-known, the .gro and .top > files are the start points for running MD simulations in GROMACS. > However, the question how to obtain the files for dendri

Re: [gmx-users] How to obtain the .gro and .top files for dendrimers

wuxiao wrote: Dear gmx users, On current, I plan to study a dendrimer (like PAMAM) using MD simulations available in GROMACS. As is well-known, the .gro and .top files are the start points for running MD simulations in GROMACS. However, the question how to obtain the files for dendrimers puz

[gmx-users] How to obtain the .gro and .top files for dendrimers

Dear gmx users, On current, I plan to study a dendrimer (like PAMAM) using MD simulations available in GROMACS. As is well-known, the .gro and .top files are the start points for running MD simulations in GROMACS. However, the question how to obtain the files for dendrimers puzzles me too mu

[gmx-users] Re: Some questions about OPLS/Berger combination]

Thank you Chris for your answer. It didn't though clarify the things to me, so I'll try to explain again where my objection is. > The method is sound. A key realization is that the [ pairs ] section > defines both the LJ and the Q pairs, so we will have double of each. > We actually want double Q,

Re: [gmx-users] x2top

danilo gonzalez wrote: hi gmx-users i was reading , in other post, the posibillity to run a new molecule without create new .rtp file , but when i run that program, he gives me the next error message Program x2top, VERSION 3.3.3 Source code file: ../../../../src/kernel/x2top.c, line: 206 T