RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent

2012-02-01 Thread Pool, R.
Hi Gianluca, I have no experience with the -rerun option of mdrun, but my guess is that an integrated MC/NVT algorithm in GromPy will be faster. For CGMC, a trial configuration involves generating a new tpr file using grompp, either with N+1 or N-1 molecules of interest. I implemented such a

[gmx-users] Pulling multiple groups

2012-02-01 Thread Wright, Louise
Hi I am trying to use the pull code of gromacs (version 4.5.5) to constrain the com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group (labelled GOLD). This is the segment of the .mdp file I have used: ;CoM pull calculations pull= constraint

[gmx-users] g_analyze doubt

2012-02-01 Thread aiswarya pawar
Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how

[gmx-users] H-bonds

2012-02-01 Thread Mr Bernard Ramos
Hi everyone! I tried doing H-bond analysis using g_hbond on a solute dissolved in water. The solute has hydroxyl groups. In an attempt to analyze water-bridges formed thru H-bonds, I noticed that g_hbond does not seem to give consistent results. As previously discussed in this list, I am

Re: [gmx-users] problem with make_ndx

2012-02-01 Thread Kowsar Bagherzadeh
You should first make an *.itp file for DPPC, then include it in the *.top file. whatever that is not in GROMACS library should be defined to it. You would better see  http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf , hope it will help. From: Anushree

Re: [gmx-users] problem with make_ndx

2012-02-01 Thread Justin A. Lemkul
Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC.only I have included the name of dppc.itp file like this: This is precisely the problem - you have no DPPC in the coordinate file. ;Include DPPC chain topology #include dppc.itp

Re: [gmx-users] problem with make_ndx

2012-02-01 Thread Mark Abraham
On 1/02/2012 6:25 PM, Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC. You cannot do anything unless you have a coordinate file that includes DPPC coordinates. I don't know how to express this any more clearly. only I have

Re: [gmx-users] g_dist

2012-02-01 Thread Justin A. Lemkul
dina dusti wrote: Dear Prof. Thank you very much from your response. Yes, dist.xvg has four column consists origin distance and distances in direction x, y , z. So distance that I want according to result of g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, micelle and

[gmx-users] the DNA md simulation

2012-02-01 Thread Banafsheh Mehrazma
Dear all; Through the MD simulation for a DNA, I wonder whether we should change any options for the terminal bases or not. Thank you in advance B.Mehrazma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Pulling multiple groups

2012-02-01 Thread Justin A. Lemkul
Wright, Louise wrote: Hi I am trying to use the pull code of gromacs (version 4.5.5) to constrain the com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group (labelled GOLD). This is the segment of the .mdp file I have used: ;CoM pull calculations pull

Re: [gmx-users] g_analyze doubt

2012-02-01 Thread Justin A. Lemkul
aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided.

Re: [gmx-users] the DNA md simulation

2012-02-01 Thread Justin A. Lemkul
Banafsheh Mehrazma wrote: Dear all; Through the MD simulation for a DNA, I wonder whether we should change any options for the terminal bases or not. What is it that you think you should change? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS

Re: [gmx-users] g_analyze doubt

2012-02-01 Thread aiswarya pawar
Hi, I have used the command = g_dist -f md.xtc -s md.tpr -n index.ndx which gives an output of data= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.25299980.593 -0.203

Re: [gmx-users] g_analyze doubt

2012-02-01 Thread Mark Abraham
On 2/02/2012 12:28 AM, aiswarya pawar wrote: Hi, I have used the command = g_dist -f md.xtc -s md.tpr -n index.ndx which gives an output of data= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.000

Re: [gmx-users] g_analyze doubt

2012-02-01 Thread Justin A. Lemkul
aiswarya pawar wrote: Hi, I have used the command = g_dist -f md.xtc -s md.tpr -n index.ndx which gives an output of data= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.2529998

Re: [gmx-users] Pulling multiple groups

2012-02-01 Thread Wright, Louise
Hi Justin, thanks for your reply. Yes the distances get a lot larger and are definitely not just fluctuating. It is hard to demonstrate this without showing you the whole file which is huge. However, I have used the same input files with gromacs 4.5.4 just now and it works- I think it might

Re: [gmx-users] Pulling multiple groups

2012-02-01 Thread Justin A. Lemkul
Wright, Louise wrote: Hi Justin, thanks for your reply. Yes the distances get a lot larger and are definitely not just fluctuating. It is hard to demonstrate this without showing you the whole file which is huge. However, I have used the same input files with gromacs 4.5.4 just now and

Re: [gmx-users] g_analyze doubt

2012-02-01 Thread aiswarya pawar
If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369 SOL 20624 OW 0.785377 (nm)

Re: [gmx-users] g_analyze doubt

2012-02-01 Thread Justin A. Lemkul
aiswarya pawar wrote: If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369

Re: [gmx-users] Installing GMX-GPU 4.5.5 calculating SASA

2012-02-01 Thread lloyd riggs
So, This is slightly aside from the installation of the openMM (cuda), but is CUDA related. Does anyone know the state of the CUDA to OpenCL porting the AMD (CUDA teams said they were going to do this) and then further all CUDA work as OpenCL, as no one has mentioned anything on this since

[gmx-users] segmantation default

2012-02-01 Thread mehmet kıytak
hi all... ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı use below mdp file ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 5; 100 ps nstcomm

[gmx-users] Gromacs GPU tutorial at MD workshop

2012-02-01 Thread Berk Hess
Hi all, The NAIS Centre in Edinburgh is holding a Workshop on State-of-the-Art Algorithms for Molecular Dynamics on May 2-4. The days before this workshop, April 30-May 2, I and David Hardy from NAMD will organize a tutorial on the use of GPUs and parallel computing. Here, among other things,

[gmx-users] g_dist

2012-02-01 Thread dina dusti
Dear Prof. Thank you very much from your response. but I didn't select micelle headgroups and then terminal carbon atom but also I selected COM of micelle and for example head group of micelle! The calulation of radius of micelle by radius of gyration give that is near 2.3-2.4 nm but g_dist

Re: [gmx-users] g_rdf

2012-02-01 Thread mohammad agha
Dear Prof. Thank you very much from your reply. Is your mean that density=(N/V)*g(r), where N is the number of total atoms in box not in the shell and V is the volume of box not in the shell? Best Regards Sara From: Dallas Warren dallas.war...@monash.edu

[gmx-users] g_dist

2012-02-01 Thread dina dusti
Dear Prof. Thank you very much from your response. I removed pbc and jump in my system, and when I see my system as visual in ngmx, there is not pbc and jump and has been created one micelle and it remain stable for long times. I really don't know what should I do! Best Regards Dina --

[gmx-users] Gromacs analysis tools for Namd output

2012-02-01 Thread PAUL NEWMAN
Dear Gromacs users, I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I just installed Gromacs 4.5.4 and it works well. In addition I installed VMD 1.9 and set up VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is located the dcdplugin.so

Re: [gmx-users] segmantation default

2012-02-01 Thread Justin A. Lemkul
mehmet kıytak wrote: hi all... ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı use below mdp file Please post a complete .mdp file. The Unix 'cat' command can be used to print the contents of the text file, which can then be copied and pasted into an email.

Re: [gmx-users] g_dist

2012-02-01 Thread Justin A. Lemkul
dina dusti wrote: Dear Prof. Thank you very much from your response. but I didn't select micelle headgroups and then terminal carbon atom but also I selected COM of micelle and for example head group of micelle! The calulation of radius of micelle by radius of gyration give that is near

[gmx-users] g_dist

2012-02-01 Thread dina dusti
Dear Prof. Thank you very much for your help. Yes, I also used from g_rdf and g_gyrate but I am seeking root-mean-square distance that there is in many articles for calculation of radius of micelle and radius of dry core (hydrocarbone). I understood that they used g_dist but it doesn't work

Re: [gmx-users] g_dist

2012-02-01 Thread Justin A. Lemkul
dina dusti wrote: Dear Prof. Thank you very much for your help. Yes, I also used from g_rdf and g_gyrate but I am seeking root-mean-square distance that there is in many articles for calculation of radius of micelle and radius of dry core (hydrocarbone). I understood that they used g_dist

[gmx-users] g_dist

2012-02-01 Thread dina dusti
Dear Prof. Thank you very much from your response. He answer me that I should use from g_gyration for radius of micelle, but what should I do for hydrocarbon (dry) core or calculation of inner core of micelle (i.e. the first of carbon on tail of surfactant with COM of micelle)? Best Regards

Re: [gmx-users] segmantation default

2012-02-01 Thread mehmet kıytak
hi justin ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron distance edge 2.0 nm. ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 250 ; 5 ns nstcomm

Re: [gmx-users] segmantation default

2012-02-01 Thread Justin A. Lemkul
mehmet kıytak wrote: hi justin ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron distance edge 2.0 nm. No, that's almost certainly not the problem. Insufficient minimization/equilibration, or instability due to the use of the free energy code is more

Re: [gmx-users] g_dist

2012-02-01 Thread Justin A. Lemkul
dina dusti wrote: Dear Prof. Thank you very much from your response. He answer me that I should use from g_gyration for radius of micelle, but what should I do for hydrocarbon (dry) core or calculation of inner core of micelle (i.e. the first of carbon on tail of surfactant with COM of

Re: [gmx-users] g_analyze doubt

2012-02-01 Thread Mark Abraham
On 2/02/2012 2:08 AM, aiswarya pawar wrote: If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596

Re: [gmx-users] Gromacs analysis tools for Namd output

2012-02-01 Thread Mark Abraham
On 2/02/2012 4:35 AM, PAUL NEWMAN wrote: Dear Gromacs users, I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I just installed Gromacs 4.5.4 and it works well. In addition I installed VMD 1.9 and set up

RE: [gmx-users] g_rdf

2012-02-01 Thread Dallas Warren
d(r) = (N/V)*g(r) Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer,

[gmx-users] Minimization Problems

2012-02-01 Thread Alex Seling
Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size for a few interactions, with each of them approaching inf.

Re: [gmx-users] Minimization Problems

2012-02-01 Thread lina
On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling selin...@msu.edu wrote: Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase

Re: [gmx-users] Minimization Problems

2012-02-01 Thread Mark Abraham
On 2/02/2012 3:36 PM, Alex Seling wrote: Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size for a few

Re: [gmx-users] Minimization Problems

2012-02-01 Thread Mark Abraham
On 2/02/2012 3:42 PM, lina wrote: On Thu, Feb 2, 2012 at 12:36 PM, Alex Selingselin...@msu.edu wrote: Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp

Re: [gmx-users] problem with make_ndx

2012-02-01 Thread Anushree Tripathi
Please suggest me the exact way to include dppc coordinates in topol.top file. On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/02/2012 6:25 PM, Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC.

Re: [gmx-users] problem with make_ndx

2012-02-01 Thread Peter C. Lai
Are you actually trying to simulate a membrane protein inside a DPPC bilayer though? If not, what is your reason for having it in your system? Also the topol.top file does not contain coordinates at all, only the forcefield parameterization. On 2012-02-02 12:11:44PM +0530, Anushree Tripathi

Re: [gmx-users] problem with make_ndx

2012-02-01 Thread Mark Abraham
On 2/02/2012 5:41 PM, Anushree Tripathi wrote: Please suggest me the exact way to include dppc coordinates in topol.top file. Start here http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations, as I think Justin already suggested. You should definitely learn (about) other people's

Re: [gmx-users] problem with make_ndx

2012-02-01 Thread Anushree Tripathi
Yes I want to simulate the protein inside DPPC bilayer but how could I make the index file. Everytime it is showing error that no DPPC found in index file. On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai p...@uab.edu wrote: Are you actually trying to simulate a membrane protein inside a DPPC

[gmx-users] how to make the SiO2 host to be neutral ?

2012-02-01 Thread Kiwoong Kim
Hi, I'm studying the diffusion system of some guest into zeolite structure (SiO2) assumed to be rigid body. My question is about making the host neutral. I obtained the unit cell of zeolite structure from the web. The structure exhibit net charge. (If I give some charge to Si and O which

Re: [gmx-users] problem with make_ndx

2012-02-01 Thread Peter C. Lai
Ok. You will: 1. Need an actual DPPC bilayer. You can either make one from scratch (using something like VMD), or use pre-equilibrated patches from other people (like the ones from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) (dppc128.pdb from that site). 2a. The