[gmx-users] Defined number of molecule of water into box

I solved with genbox -cp conf.gro -cs -maxsol 100 -p topol.top -o out.gro Thanks! Anna-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Pleas

[gmx-users] implicit water and a layer of explicit water molecule

Dear all, I got some question about the implicit solvent.1) In gromacs, is it possible simulate a protein in a layer of explicit water, and put this system (protein + SOL) into a big box and make the MD simulation with implicit solvent? How I have to set the md.mdp parameter (; IMPLICIT SOLVE

Re: [gmx-users] implicit water and a layer of explicit water molecule

On 4/04/2011 6:11 PM, battis...@libero.it wrote: Dear all, I got some question about the implicit solvent. 1) In gromacs, is it possible simulate a protein in a layer of explicit water, and put this system (protein + SOL) into a big box and make the MD simulation with implicit solvent?

[gmx-users] Setting the C6 LJ term for OPLSA FF

Dear all I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF. In particular I want to set the attractive part of the LJ potential to zero (C6=0). In doing this I have read the manual but unfortunately the reported explanation did not help me. To understand how it works i

Re: [gmx-users] Setting the C6 LJ term for OPLSA FF

On 4/04/2011 6:55 PM, Luca Bellucci wrote: Dear all I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF. In particular I want to set the attractive part of the LJ potential to zero (C6=0). In doing this I have read the manual but unfortunately the reported explanation did

R: [gmx-users] implicit water and a layer of explicit water molecule

Dear Mark, about point 2, yes I need to have a uniform distribution of a defined numberof water molecule (eg. 100 water molecule ) into my box. Is it possible with genbox? After, I'll have to make the md simulation for my system in implicit solvent (I'll have "protein + 100 molecule SOL + impl

Re: R: [gmx-users] implicit water and a layer of explicit water molecule

On 4/04/2011 7:12 PM, battis...@libero.it wrote: Dear Mark, about point 2, yes I need to have a uniform distribution of a defined number of water molecule (eg. 100 water molecule ) into my box. Is it possible with genbox? Yes, but not by starting with a uniform distribution of a condensed-pha

[gmx-users] FEP and loss of performance

Dear all, when I run a single free energy simulation i noticed that there is a loss of performace with respect to the normal MD free_energy= yes init_lambda= 0.9 delta_lambda = 0.0 couple-moltype = Protein_Chain_P couple-lambda0 = vdw-q couple-lambda0 = none couple-intramol= yes

R: [gmx-users] implicit water and a layer of explicit water molecule

Thank you very much for your suggestions! Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the li

[gmx-users] Check out my photos on Facebook

Hi Gmx-users, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Gokul To sign up for Facebook, follow the link below: ht

[gmx-users] Check out my photos on Facebook

Hi Gmx-users, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Gokul To sign up for Facebook, follow the link below: ht

Re: [gmx-users] Umbrella Sampling

Hi I assume that the order of the file names in the tpr-files.dat and pullx-files.dat is irrelevant for g_wham . Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Maili

Re: [gmx-users] Umbrella Sampling

From g_wham -h: "The tpr and pullx files must be in corresponding order, i.e. the first tpr created the first pullx, etc." -Justin Gavin Melaugh wrote: Hi I assume that the order of the file names in the tpr-files.dat and pullx-files.dat is irrelevant for g_wham . Cheers Gavin -- =

[gmx-users] minimization and simulation problems

Dear all, I'm trying to run simulation of 30 proteins in water using the Martini force field. I used water.gro file in order to solvate the proteins. For minimization I used the em.mdp file published at Martini site (http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol par

[gmx-users] FEP and loss of performance

If we accept your text at face value, then the simulation slowed down by a factor of 1500%, certainly not the 16% of the load balancing. Please let us know what version of gromacs and cut and paste your cammands that you used to run gromacs (so we can verify that you ran on the same number

[gmx-users] minimization and simulation problems

What are your initial box dimensions prior to em? Also, please copy and paste your .mdp options. Also, what happens when you run the same post-em simulation with nsteps=1 ? -- original message -- Dear all, I'm trying to run simulation of 30 proteins in water using the Martini force field. I

Re: [gmx-users] Umbrella Sampling

Hi Justin Yeah I know the tpr files must be in corresponding order with pullx.xvg files. What I meant was should they be in order of distance. i.e say If my windows go from 0 to 1.0 nm with windows every 0.1nm, could I list the files in any order or does it have to like 0.1 0.2 0.3 0.4 Gavin

Re: [gmx-users] Umbrella Sampling

Gavin Melaugh wrote: Hi Justin Yeah I know the tpr files must be in corresponding order with pullx.xvg files. What I meant was should they be in order of distance. i.e say If my windows go from 0 to 1.0 nm with windows every 0.1nm, could I list the files in any order or does it have to like 0.

Re: [gmx-users] minimization and simulation problems

my box dimensions are 368A Quoting chris.ne...@utoronto.ca: What are your initial box dimensions prior to em? Also, please copy and paste your .mdp options. Also, what happens when you run the same post-em simulation with nsteps=1 ? -- original message -- Dear all, I'm trying to run sim

Re: [gmx-users] FEP and loss of performance

Hi Chris, thank for the suggestions, in the previous mail there is a mistake because couple-moltype = SOL (for solvent) and not "Protein_chaim_P". Now the problem of the load balance seems reasonable, because the water box is large ~9.0 nm. However the problem exist and the performance loss is v

Re: [gmx-users] FEP and loss of performance

Luca Bellucci wrote: Hi Chris, thank for the suggestions, in the previous mail there is a mistake because couple-moltype = SOL (for solvent) and not "Protein_chaim_P". Now the problem of the load balance seems reasonable, because the water box is large ~9.0 nm. Now your outcome makes a lo

[gmx-users] FEP and loss of performance

Load balancing problems I can understand, but why would it take longer in absolute time? I would have thought that some nodes would simple be sitting idle, but this should not cause an increase in the overall simulation time (15x at that!). There must be some extra communication? I agree with

Re: [gmx-users] FEP and loss of performance

Dear Chris and Justin Thank you for your precious suggestions This is a test that i perform in a single machine with 8 cores and gromacs 4.5.4. I am trying to enhance the sampling of a protein using the decoupling scheme of the free energy module of gromacs. However when i decouple only the

[gmx-users] g_mdmat distance matrices

Dear gmx users, I used g_mdmat and have got a distance matrices in .xpm format. Now I want to compare two matrices: for a protein var1 and for protein var2 and create one output file with this compare. How can I do it? If there is no such function in gromacs, how can I convert .xpm format to get

Re: [gmx-users] minimization and simulation problems

Quoting pol...@fh.huji.ac.il: Dear gromacs users, my box dimensions are 368A and when I run the simulation with nsteps=1 it works fine. The mdp files used for minimization and post-em simulation are attached. Thanks again for your help. Regina Quoting chris.ne...@utoronto.ca: What are you

[gmx-users] minimization and simulation problems

Can you please redo the md part with gen_vel=yes and see if that makes any difference? Generally, you need to narrow down the problem for us. Does it crash in serial as well as parallel? How many steps does it go before the crash? what happens to the system volume as a function of time for the

Re: [gmx-users] FEP and loss of performance

Luca Bellucci wrote: Dear Chris and Justin Thank you for your precious suggestions This is a test that i perform in a single machine with 8 cores and gromacs 4.5.4. I am trying to enhance the sampling of a protein using the decoupling scheme of the free energy module of gromacs. However

[gmx-users] FEP and loss of performance

>> Dear Chris and Justin / Thank you for your precious suggestions />>/ This is a test that i perform in a single machine with 8 cores />>/ and gromacs 4.5.4. />>/ />>/ I am trying to enhance the sampling of a protein using the decoupling scheme />>/ of the free energy module of gromacs

Re: [gmx-users] FEP and loss of performance

Chris Neale wrote: >> Dear Chris and Justin / Thank you for your precious suggestions />>/ This is a test that i perform in a single machine with 8 cores />>/ and gromacs 4.5.4. />>/ />>/ I am trying to enhance the sampling of a protein using the decoupling scheme />>/ of the free ener

[gmx-users] autocorrelation functions

Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to m

[gmx-users] how to Installing GROMACS in rocks cluster

Dear Colleagues. I have been searching information about "HOW TO INSTALL GROMACS in rocks cluster?". Unfortunately, the information that I found is not clear. Someone can help me with this question. Maybe there are basic but important steps that I have to keep in mind. Could you please share your

[gmx-users] autocorrelation functions

Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to mo

Re: [gmx-users] FEP and loss of performance

Yes i am testing the possibility to perform an Hamiltonian-REMD Energy barriers can be overcome increasing the temperature system or scaling potential energy with a lambda value, these methods are "equivalent". Both have advantages and disavantages, at this stage it is not the right place to de

[gmx-users] g_chi

Hi, I have 2 questions on using g_chi to calculate only one omega angle for X-Pro. 1. I used the following command: "g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg" and got the following message: Fatal error: Library file in current dir nor  not found aminoacids.datin default directories. (You

Re: [gmx-users] g_chi

Hi Simon, Regarding the first question you should set GMXLIB as $GMXDATA/gromacs/top. I don't know how to solve the second problem bacause I never used g_chi Il 04/04/2011 22:19, simon sham ha scritto: Hi, I have 2 questions on using g_chi to calculate only one omega angle for X-Pro. 1. I us

Re: [gmx-users] g_chi

simon sham wrote: Hi, I have 2 questions on using g_chi to calculate only one omega angle for X-Pro. 1. I used the following command: "g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg" and got the following message: Fatal error: Library file in current dir nor not found aminoacids.datin

[gmx-users] Postdoc position available

Hi all, A post-doctoral research position is available at Northwestern University at Evanston, IL. The position is in the field of computational physical chemistry, with a focus on molecular dynamics simulation and force field development. The systems to be studied include water/air, water/ic

[gmx-users] coordination number and g_analysis

Hello, I want to calculat the coordination number of solute in first solvation shell. integration of (4*pi*r^2*g(r)) from 0 to 2.6 A(first solvation shell) If I calcualte the g_rdf for first solvation shell (till 2.6 A) and then I integrate this using g_analysis. Can I go this way. Nilesh -

[gmx-users] Re: gmx-users Digest, Vol 84, Issue 28

is question. Maybe there are basic but important > steps that I have to keep in mind. Could you please share yours > experiences? > > > Thank you in advance. > > Miguel Quiliano. > > P.D I have installed rocks cluster 5.4 > -- next part -- > An HTML

Re: [gmx-users] Re: gmx-users Digest, Vol 84, Issue 28

. Maybe there are basic but important steps that I have to keep in mind. Could you please share yours experiences? Thank you in advance. Miguel Quiliano. P.D I have installed rocks cluster 5.4 -- next part -- An HTML attachment was scrubbed..

Re: [gmx-users] coordination number and g_analysis

I'll rather use: g_rdf -cn Marcelo. On Apr 4, 2011, at 4:17 PM, Nilesh Dhumal wrote: Hello, I want to calculat the coordination number of solute in first solvation shell. integration of (4*pi*r^2*g(r)) from 0 to 2.6 A(first solvation shell) If I calcualte the g_rdf for first solvation sh

Re: [gmx-users] Splitted DMPC bilayer

Justin, Thank you for your comments after finishing the MD production run for up to 20 ns... Since this step was over very quickly, now I have a simple question ¿How long, in human time, should a production run last? The production run was carried out in six processors Intel Xeon (R) E540

Re: [gmx-users] Splitted DMPC bilayer

Dr. Ramón Garduño-Juárez wrote: Justin, Thank you for your comments after finishing the MD production run for up to 20 ns... Since this step was over very quickly, now I have a simple question ¿How long, in human time, should a production run last? There is no way to answer that. It

[gmx-users] g_chi

Hi, Thanks for those who replied my previous questions on g_chi. I just installed the latest version of gromacs 4.5.4 and could run the command. I still have a question about the command: Again, I used the following command: "g_chi -s md.tpr -f md.xtc -omega" It generated a series of xmgrace file

Re: [gmx-users] Splitted DMPC bilayer

Justin, Again much obliged for your comments. They are most illustrative... I would like to make a final note on the issue of these many e-mails... I am sure that GROMACS is fast, but that fast?... For the sake of knowing that we are doing the right things, this is our topol.top file in which

Re: [gmx-users] Splitted DMPC bilayer

Dr. Ramón Garduño-Juárez wrote: Justin, Again much obliged for your comments. They are most illustrative... I would like to make a final note on the issue of these many e-mails... I am sure that GROMACS is fast, but that fast?... Yes. Your results prove it. With quality hardware, you ge

Re: [gmx-users] g_chi

simon sham wrote: Hi, Thanks for those who replied my previous questions on g_chi. I just installed the latest version of gromacs 4.5.4 and could run the command. I still have a question about the command: Again, I used the following command: "g_chi -s md.tpr -f md.xtc -omega" It generated a

Re: [gmx-users] autocorrelation functions

On 5/04/2011 2:55 AM, shivangi nangia wrote: Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelati

[gmx-users] Protein_thermal_Unfolding

Dear users, I am new to Gromacs. I am trying to study thermal unfolding of a protein having intra molecular disulfide bonds. As during simulations these bonds will not break, will I be able to study the unfolding pathway. Are there other ways to study such type of systems. S Satya Gulbraga Univers

Re: [gmx-users] the total charge of system is not an integer

Dear Tsjerk, Hi Ahmet, > > As suggested, it's better to break up your molecule into smaller > charge groups. Note that charge groups don't need to have zero charge, > nor integer charge. In your case, I'd suggest two COH groups for EDO, > which will have zero net charge each, and for TRS I'd take

Re: [gmx-users] the total charge of system is not an integer

On 5/04/2011 3:57 PM, ahmet yıldırım wrote: Dear Tsjerk, Hi Ahmet, As suggested, it's better to break up your molecule into smaller charge groups. Note that charge groups don't need to have zero charge, nor integer charge. In your case, I'd suggest two COH groups for EDO, wh

[gmx-users] Invalid order for directive atomtypes

hello friends, I am doing simulation of ganglioside gm2 and am getting the following error. Fatal error: Syntax error - File gm2gang.top, line 6 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Can anyone please help me in this.I am new to gromacs. -- *Geethu Issac* * "A