Re: [gmx-users] searching mailing lists other than gmx-users

Hi, Sure, but the only other list worth searching is the developers list. Rossen Mark Abraham wrote: Hi, As far as I can see, the mailing list search page http://www.gromacs.org/Support/Mailing_Lists/Search only searching gmx-users. While that's a good start, there's often information on th

RE: [gmx-users] trjcat xtc files

Your second guess is correct! I used grompp to restart (I had thought it might provide me with the chance to change things if needed). I was surprised initially when "cat" command did not work! The number of frames were most of the time less than what it should be. I also checked the 'trjcat -h'. I

Re: [gmx-users] trjcat xtc files

Paymon Pirzadeh wrote: Sorry, My command line was: trjcat_d_mpi -f AFPI_Ih1010_54_58_Npt265_2.xtc AFPI_Ih1010_54_58_Npt265_3.xtc AFPI_Ih1010_54_58_Npt265_4.xtc AFPI_Ih1010_54_58_Npt265_5.xtc AFPI_Ih1010_54_58_Npt265_6.xtc -o AFPI_Ih1010_54_58_Npt265_merged2-6.xtc the "_d_mpi" is the suffix use

Re: [gmx-users] trjcat xtc files

Sorry, My command line was: trjcat_d_mpi -f AFPI_Ih1010_54_58_Npt265_2.xtc AFPI_Ih1010_54_58_Npt265_3.xtc AFPI_Ih1010_54_58_Npt265_4.xtc AFPI_Ih1010_54_58_Npt265_5.xtc AFPI_Ih1010_54_58_Npt265_6.xtc -o AFPI_Ih1010_54_58_Npt265_merged2-6.xtc the "_d_mpi" is the suffix used for double precision an

Re: [gmx-users] trjcat xtc files

Paymon Pirzadeh wrote: Hello, I am trying to concatenate several xtc files. When I use the trjcat, it only writes the last file into the output file! where the problem could be? In your command line. Why didn't you tell us what it was? :-) Mark ___ g

[gmx-users] trjcat xtc files

Hello, I am trying to concatenate several xtc files. When I use the trjcat, it only writes the last file into the output file! where the problem could be? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Daniel Adriano Silva M wrote: Mark, Again me. I reinstalled things, you must be thinking that I am wrong trying to get the icc installation to work, but as I stated on a previous mail I get very good scaling and over 40% better performance with icc than gcc. I had tested gmx_test, and all appear

Re: [gmx-users] Adsorption energy of a single molecule

Darrell Koskinen wrote: Hi Justin, Since I cannot use the original .tpr file, then do I need to run grompp with the new index file to create a "new" .tpr file, "mdtopolnew.tpr"? I assume I then need to modify the energygrps line within the .mdp file to include these new energy groups and the

[gmx-users] Adsorption energy of a single molecule

Hi Justin, Since I cannot use the original .tpr file, then do I need to run grompp with the new index file to create a "new" .tpr file, "mdtopolnew.tpr"? I assume I then need to modify the energygrps line within the .mdp file to include these new energy groups and then execute "mdrun -rerun mdtr

[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

Hi Mark, By "missing", I meant zero by design. I found the initial opls paper in which the H atom in ammonia is assigned a zero LJ parameter and the entire LJ parameter for ammonia is assigned to the N atom. I was just wondering if assigning the entire LJ parameter to the N atom might affect

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Mark, Again me. I reinstalled things, you must be thinking that I am wrong trying to get the icc installation to work, but as I stated on a previous mail I get very good scaling and over 40% better performance with icc than gcc. I had tested gmx_test, and all appears to be ok, but I think the gmx

Re: [gmx-users] Adsorption energy of a single molecule

Darrell Koskinen wrote: Hi Justin, In my simulation, I have just over 100 ammonia molecules and, of these molecules, 10 to 20 adsorb onto the graphene sheet. I initially thought that I would need to tag each one of the ammonia molecules, since I would not know, in advance of running the simul

Re: [gmx-users] Adsorption energy of a single molecule

Darrell Koskinen wrote: Hi Justin, In my simulation, I have just over 100 ammonia molecules and, of these molecules, 10 to 20 adsorb onto the graphene sheet. I initially thought that I would need to tag each one of the ammonia molecules, since I would not know, in advance of running the sim

[gmx-users] Adsorption energy of a single molecule

Hi Justin, In my simulation, I have just over 100 ammonia molecules and, of these molecules, 10 to 20 adsorb onto the graphene sheet. I initially thought that I would need to tag each one of the ammonia molecules, since I would not know, in advance of running the simulation, which of these mo

[gmx-users] searching mailing lists other than gmx-users

Hi, As far as I can see, the mailing list search page http://www.gromacs.org/Support/Mailing_Lists/Search only searching gmx-users. While that's a good start, there's often information on the other lists people might wish the option of searching for. Can we have more of a user interface here,

Re: [gmx-users] Modify disre_fc during md

Andrei Istrate wrote: Hello all, I would like to modify the force constant of some distance constraints during my MD. I know this is not implemented in GROMACS and I'd like to modify the code. I have read that it could be done in md.c, but I didn't find the variable dr_fc in this file. Why a

Re: [gmx-users] Quick question about g_mindist

ms wrote: Hi, I am using g_mindist to see how close get C-alphas to each other in my chains. What I do is selecting C-alpha two times when prompted. I have only a quick question, just to be sure: The script doesn't take into account the distance between *neighbouring C-alpha*, isn't it? I d

[gmx-users] Modify disre_fc during md

Hello all, I would like to modify the force constant of some distance constraints during my MD. I know this is not implemented in GROMACS and I'd like to modify the code. I have read that it could be done in md.c, but I didn't find the variable dr_fc in this file. Tell me please what variable

[gmx-users] Quick question about g_mindist

Hi, I am using g_mindist to see how close get C-alphas to each other in my chains. What I do is selecting C-alpha two times when prompted. I have only a quick question, just to be sure: The script doesn't take into account the distance between *neighbouring C-alpha*, isn't it? thanks! m. __

Re: Fwd: Fwd: [gmx-users] scripts to generate topology CG

Francesco Pietra wrote: I was asked to submit details of the procedure to get a solvated CG system in order to see if help to correct the procedure is feasible. Is the described procedure still insufficient? thanks for answering I posted several suggestions and some questions when you last po

Re: [gmx-users] Is anyone also using lammps?s

Peng Yi wrote: Thank for your reply! I have done some NVT runs per your suggestion, and the results are similar to NPT runs, i.e., Gromacs results is more affected by changing integration timestep than Lammps. Details below: A melt of 240 octane chains by united-atom model. T=300K, V=55.46 nm

Fwd: Fwd: [gmx-users] scripts to generate topology CG

I was asked to submit details of the procedure to get a solvated CG system in order to see if help to correct the procedure is feasible. Is the described procedure still insufficient? thanks for answering francesco -- Forwarded message -- From: Francesco Pietra Date: Sun, Oct 25,

Re: [gmx-users] Is anyone also using lammps?s

Thank for your reply! I have done some NVT runs per your suggestion, and the results are similar to NPT runs, i.e., Gromacs results is more affected by changing integration timestep than Lammps. Details below: A melt of 240 octane chains by united-atom model. T=300K, V=55.46 nm^3. Both Gromacs

Re: [gmx-users] conf.gro file

leila karami wrote: Hi what is difference between input.gro and conf.gro files? No clue. What are you doing? -Justin ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] conf.gro file

Hi what is difference between input.gro and conf.gro files? ___ 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 po

Re: [gmx-users] PMF and Gromacs 4

Rebeca García Fandiño wrote: Hi, I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the Gromacs list that the pull code had been completely rewritten in the new version of Gromacs, but I cannot find much information about the new way to use this. Reading the manua

[gmx-users] PMF and Gromacs 4

Hi, I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the Gromacs list that the pull code had been completely rewritten in the new version of Gromacs, but I cannot find much information about the new way to use this. Reading the manual (pag 280) I can see: “The option

Re: [gmx-users] Fw: help for installing gromacs with cpmd

Thank You Mark. -- On Sun, 11/1/09, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] Fw: help for installing gromacs with cpmd To: "Discussion list for GROMACS users" Date: Sunday, November 1, 2009, 4:59 PM Farzad Molani wrote: > Hi, Yes I read some articles and search in goog

Re: [gmx-users] Fw: help for installing gromacs with cpmd

Farzad Molani wrote: Hi, Yes I read some articles and search in google but I couldn't get enough information about that. thanks. There's nobody here being paid to guess what your problem is :-) There's a page listed on google with explicit installation instructions. If you have a specific pr

Re: [gmx-users] Fw: help for installing gromacs with cpmd

Hi, Yes I read some articles and search in google but I couldn't get enough information about that. thanks. --- On Sun, 11/1/09, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] Fw: help for installing gromacs with cpmd To: "Discussion list for GROMACS users" Date: Sunday, No

Re: [gmx-users] Fw: help for installing gromacs with cpmd

Farzad Molani wrote: Hi. I am going to install gromacs with cpmd but I do'nt know what do am I? What do I need for installing? what about EGO? your sincereliy Farzad Did you start by searching the web? http://www.google.com.au/search?q=cpmd+gromacs Mark

Re: [gmx-users] Adsorption energy of a single molecule

Darrell Koskinen wrote: Hi Justin, Thanks for the suggestion. I looked through the GROMACS manual and the only method I can see of obtaining the adsorption energy between an adsorbed ammonia molecule and the graphene sheet would be to create an index file that assigns a separate index for ea

[gmx-users] Fw: help for installing gromacs with cpmd

Hi. I am going to install gromacs with cpmd but I do'nt know what do am I? What do I need for installing? what about EGO? your sincereliy Farzad ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

Re: [gmx-users] gmx user

pawan raghav wrote: Dear all, I am a new user of GROMACS and suffering from severe problem about fftw-3.2.2 installation. Actually I have installed cygwin on windows XP with gcc, gdb, and make packages rest all are leaved default. Now when I have used configure command then it would give las

[gmx-users] gmx user

Dear all, I am a new user of GROMACS and suffering from severe problem about fftw-3.2.2 installation. Actually I have installed cygwin on windows XP with gcc, gdb, and make packages rest all are leaved default. Now when I have used configure command then it would give last line as config.status:

Re: [gmx-users] S-type Hydrogen bond correlation function

Thank you. Since i am using gromacs version 3.3.1 i facing the problem in getting the trajectory output with the option -r as given in the thread, http://www.mail-archive.com/gmx-users@gromacs.org/msg01629.html Is there any alternative way to solve the problem... rama On Sun, Nov 1, 2009 at 12:43

Re: [gmx-users] S-type Hydrogen bond correlation function

Ramachandran G wrote: Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama You could try the trjorder program O

Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

Darrell Koskinen wrote: Hi Mark, I thought opls_127 and opls_128 were the representative atoms to use for ammonia. Please correct me if I am wrong. I don't know anything more than what's in ffoplsa* files or the papers. Would the adsorption of the polar ammonia molecule onto the polar (hydro

Re: [gmx-users] S-type Hydrogen bond correlation function

Dear David, Thank you for you help. It is very much helpful for me. I have one more question. Is it possible to create index file for the oxygen atom or water molecules alone exist in a hydration shell. Thank you again. Rama On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel wrote: > Rama