[gmx-users] mdatoms-massA pointer dereferencing

Good morning! I'm having C trouble with something which should be simple enough: GROMACS uses a struct called mdatoms which, amongst other things, houses the atom masses during the simulation. I'm trying to access this data (an array of the masses of all atoms). I've tried to consult internet

[gmx-users] Post processing in Gromacs code

Dear Gromacs users, Where Can I find the code for the post processing functions in Gromacs. I want to modify the code like for the g_dist and other functions. I tried on the bin in gromacs but cannot open it and view the code inside there. Can you please tell me on that. Rob --

[gmx-users] FTP Server not working?

Hello, I am trying to download Version 4.0.5 but the FTP server keeps timing out. Is there a problem? Thanks, Mark -- Mark Patrick Cheeseman Computational Scientist KSL (KAUST Supercomputing Laboratory) Building 1, Office #126 King Abdullah University of Science Technology Thuwal 23955-6900

RE: [gmx-users] mdatoms-massA pointer dereferencing

Hi, massA and massB in mdatoms are only set when doing free-energy calculations. massT gives the mass of a particle. Unfortunately there is a serious lack of documentation in the data type include files (and in most other parts of the code). Berk Date: Tue, 31 Aug 2010 10:46:51 +0300 From:

RE: [gmx-users] Distance from heavy atom to Methyl Vsite

Hi, The distance component along the O-C bond is the distance between O and the COM of CH3. The distance component perpendicular to the O-C bond is such that the intertia (sum m r^2) of the two masses matches that of the 3 H's. I can mail you an awk script that automatically determines this

[gmx-users] Fatal error when using do_dssp

Hi,  I have installed the dsspcmbi, and then add  export  DSSP=/home/hzj1000/dssp，I can use dsspcmbi.But when I use do_dssp, came across the following error: Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null 2 /dev/null   Please help me, thanks ! Zhongjin He

Re: [gmx-users] Post processing in Gromacs code

- Original Message - From: tekle...@ualberta.ca Date: Tuesday, August 31, 2010 17:50 Subject: [gmx-users] Post processing in Gromacs code To: Discussion list for GROMACS users gmx-users@gromacs.org Dear Gromacs users, Where Can I find the code for the post processing functions in

Re: [gmx-users] Fatal error when using do_dssp

- Original Message - From: zhongjin zhongjin1...@yahoo.com.cn Date: Tuesday, August 31, 2010 18:23 Subject: [gmx-users] Fatal error when using do_dssp To: gmx-users@gromacs.org --- | Hi, I have installed the dsspcmbi, and then

Re: [gmx-users] g_hbond

Nilesh Dhumal wrote: THanks. I have one more system dioxin + water molecules. There is possiblity of C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water. I want to calculate the number of hydrogen bonds. I used the following command g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr

Re: [gmx-users] FTP Server not working?

Hi Mark, I've just tried the link you mentioned and it seems to work. Could you try again? Cheers, -- Szilárd On Tue, Aug 31, 2010 at 9:53 AM, Mark Cheeseman mark.cheese...@kaust.edu.sa wrote: Hello, I am trying to download Version 4.0.5 but the FTP server keeps timing out. Is there a

[gmx-users] Problems with GPU-Version and implicit water models

Dear all, I am using Gromacs-4.5-beta4 and compiled the GPU-Version. So far only Amber-FF are working in the GPU-version. When I want to use the GBSA implicit water-model I have to use cut-off for the electrostatic interactions due to this error-message: ERROR 1 [file PR.mdp]: With GBSA,

[gmx-users] Re: Re[7]: Flat energy profile in g_wham

Sorry Alex, but there is no good substitute what I have already suggested. I helped you find a lead and I suggested a way to simplify your system to discover what is going on. Now it's up to you to do that work. It might end up being a bug, but I doubt it. I have done things similar to

[gmx-users] pbc in one direction only for analysis?

Dear gromacs users I have surface groups anchored on a cylindrical pore wall (similar to a carbon nanotube). The pore runs along the z direction. I am trying to determine to what extent my surface groups are clustered together and was thinking of using g_mindist and/or g_rdf for this

[gmx-users] pbc in one direction only for analysis?

It's a messy solution, but you could 1. run trjconv so that your cylinder is in the unit cell 2. convert your trajectory to .gro files 3. massively expand the x and y dimensions of each .gro 4. join the .gros to a .xtc 5. g_rdf You could also use template.c to write a program that does this

Re: [gmx-users] g_hbond

Justin A. Lemkul skrev 2010-08-31 12.35: Nilesh Dhumal wrote: THanks. I have one more system dioxin + water molecules. There is possiblity of C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water. I want to calculate the number of hydrogen bonds. I used the following command

[gmx-users] deletion of some water molecules

Dear gromacs users I did simulation of protein-dna complex in a box with size 7,7,7. There are 5000 water molecule in this box. After full md simulation, I need a pdb or gro file containing only water molecules being exactly environment of pr-dna complex and not water molecules being in edges

Re: [gmx-users] deletion of some water molecules

leila karami skrev 2010-08-31 14.48: Dear gromacs users I did simulation of protein-dna complex in a box with size 7,7,7. There are 5000 water molecule in this box. After full md simulation, I need a pdb or gro file containing only water molecules being exactly environment of pr-dna

Re: [gmx-users] deletion of some water molecules

You can use trjorder to do this Cheers Tom leila karami wrote: Dear gromacs users I did simulation of protein-dna complex in a box with size 7,7,7. There are 5000 water molecule in this box. After full md simulation, I need a pdb or gro file containing only water molecules being exactly

[gmx-users] Different impacts in the pressure

Dear Gromacs users, I am quite new in gromacs, so maybe I am missing something obvious. Is there any standard option/function to calculate different impacts into the pressure tensor (i.e. due to VdW interactions, due to bonded interaction, due to electrostatics etc.) ? Thanks a lot in advance,

[gmx-users] deletion of some water molecules

Dear Erik Marklund thabks for your attention I want only have water molecules being in 1.5 nm of solute in final frame (2 ps) I used following command: trjorder -f *.xtc -s *.tpr -n *.ndx -o *.gro -r 1.5 -b 2 is it true? -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Multiple nrexcl commands in GROMACS

Hello, We are trying to create a model of a carbon nanotube with simple carbon-like chains attached around the entrance and exit of the nanotube. The problem is we need nrexcl set to 3 in nanotube but wnat nrexcl=1 in the chains. We have searched the GROMACS manual and user list extensively

Re: [gmx-users] Multiple nrexcl commands in GROMACS

On 2010-08-31 16.23, WJ Evans wrote: Hello, We are trying to create a model of a carbon nanotube with simple carbon-like chains attached around the entrance and exit of the nanotube. The problem is we need nrexcl set to 3 in nanotube but wnat nrexcl=1 in the chains. We have searched the

[gmx-users] NAGA

Hello, I am trying to simulate N-methylglycine amide. I selected 'none' for the termini using oplsaa forcefield. I got the topology but I got the error saying: ERROR 1 [file topol.top, line 126]: No default Ryckaert-Bell. types I checked the line 126 in my topol file and it is the

[gmx-users] lipid-drug simulation question

Hi all, I am simulating drugs in water/lipid bilayer environment. And I have noticed that when I put drug into the middle of the box, it is moving rather quickly around until it finds a x or y boundary. Then it stays there moving not much on both sides of the box. In the first time it looked fine

[gmx-users] g_order question

Hello, It is said in the mannual that g_order compute the order parameter per atom for carbon tails. Can it also calculate order (degree of tetrahedrality) for water molecules if only water oxygens are selected in index file? The reference paper is for water molecules though. Also, does it

Re: [gmx-users] g_order question

On 2010-08-31 20.26, Paymon Pirzadeh wrote: Hello, It is said in the mannual that g_order compute the order parameter per atom for carbon tails. Can it also calculate order (degree of tetrahedrality) for water molecules if only water oxygens are selected in index file? The reference paper is for

[gmx-users] Re[9]: Flat energy profile in g_wham

Yep, my case is b  :(... Gromacs do writes pullx as ref COM global coords and pull COM displacement. And I still don't realize what is force value in pullf but it gives identical results for both -if and -ix options of g_wham. And g_wham do works OK at least for 2 waters separation in 0.3-1nm

[gmx-users] Re: Re[9]: Flat energy profile in g_wham

Can you post a snip of your pullx and pullf files from the water box simulation where you pulled on 2 waters? Quoting alexander yakovenko yakovenk...@ukr.net: Yep, my case is b  :(... Gromacs do writes pullx as ref COM global coords and pull COM displacement. And I still don't realize what

Re: [gmx-users] Problems with GPU-Version and implicit water models

Hi, On 08/31/2010 12:53 PM, Christian Mücksch wrote: Dear all, I am using Gromacs-4.5-beta4 and compiled the GPU-Version. So far only Amber-FF are working in the GPU-version. Gromacs-GPU supports only AMBER and CHARMM forcefields. By default, pdb2gmx enables the -cmap option, and cmap

Re: [gmx-users] g_order question

Yes, I tried it, but I run into segmentation fault. Here is part of the error message: WARNING: distance between atoms 4869 and 0 0.3 nm (3.515866). Index file might be corrupt. WARNING: distance between atoms 4870 and 0 0.3 nm (3.580329). Index file might be corrupt. WARNING: distance between

Re: [gmx-users] g_order question

On 2010-08-31 21.10, Paymon Pirzadeh wrote: Yes, I tried it, but I run into segmentation fault. Here is part of the error message: WARNING: distance between atoms 4869 and 0 0.3 nm (3.515866). Index file might be corrupt. WARNING: distance between atoms 4870 and 0 0.3 nm (3.580329). Index

Re: [gmx-users] g_order question

Here is the command: g_order_d_mpi -f 265K_50_50_50_2-pbcfixed.xtc -n wateroxygens.ndx -s 265K_50_50_50_2.tpr -o Sg265K On Tue, 2010-08-31 at 21:15 +0200, David van der Spoel wrote: On 2010-08-31 21.10, Paymon Pirzadeh wrote: Yes, I tried it, but I run into segmentation fault. Here is

Re: [gmx-users] g_order question

On 2010-08-31 21.19, Paymon Pirzadeh wrote: Here is the command: g_order_d_mpi -f 265K_50_50_50_2-pbcfixed.xtc -n wateroxygens.ndx -s 265K_50_50_50_2.tpr -o Sg265K You need to replace -o by one of -Sg sg-ang.xvg Output, Opt. xvgr/xmgr file -Sksk-dist.xvg Output, Opt. xvgr/xmgr file

[gmx-users] Re: Re[11]: Flat energy profile in g_wham

Alex, If you do decide to continue along with the method that I suggested, I'll join back in. To this point, I see no indication that you have tried to relate the force to the position for the water runs, which is my standing suggestion to you. Chris. Quoting alexander yakovenko

[gmx-users] CHARMM c36 to Gromacs

Hi, Gromacs 4.5-beta3 explicitly include the CHARMM c27 force field but not the c36 force field. Have anyone done any work to transfer the CHARMM c36 force field to Gromacs? Dr. Mark James Abraham has written a perl script to do the charmm_to_gromacs transfer, however that only works for the c27

Re: [gmx-users] g_order question

I tried the -Sg and it worked. Thanks. But, I used -Sgsl for a spatial profile and it looks like that it is not a valid option. I tried the following: g_order_d_mpi -f Ih0001_54_62_102.xtc -n wateroxygens.ndx -s Ih0001_54_62_102.tpr -os Ih0001_54_62_102-sg -sl 100 -d z but I ran into the

RE: [gmx-users] deletion of some water molecules

What happened when you tried that command? If you ran the command, tried it, and check the output to see if it is what you want, you would be a long way head of waiting hours or more for someone on the emailing list to reply with a response. Catch ya, Dr. Dallas Warren Medicinal

[gmx-users] Genbox to generate box with isolated molecules...

Dears, I'm generating a box filled with NO3 molecules using Gromacs 3.3: genbox -ci molecule.gro -p molecule.top -o bigbox.gro -box 4.0 4.0 4.0 -nmol 800 -vdwd 0.2 The file bigbox.gro is generated but molecules are entangled. This makes the geometry optimization to remove close contact

Re: [gmx-users] Genbox to generate box with isolated molecules...

Tandia, Adama wrote: Dears, I'm generating a box filled with NO3 molecules using Gromacs 3.3: Any particular reason you're using software that is five years old? Unless you've got a particular reason (i.e. continuity with older work), I'd strongly recommend upgrading to version 4.0.7