Re: [gmx-users] free energy decomposition[David Van der Spoel]

2010-10-14 Thread Sanku M
Hi David, I was trying to understand your comments little bit carefully. If it is a NVT ensemble simulation, then enthalpy becomes equal to potential energy ( as the work due to volume-change is zero ). But, I was wondering about your other comment: i.e. if it is constraint method, the pot

Re: [gmx-users] Is there a publication of the implemented reaction-field method?

2010-10-14 Thread Mark Abraham
On 15/10/2010 1:12 AM, Sascha Rehm wrote: Dear all, to deal with my long-range interactions I used the reaction-field-zero method. Therefore I searched for a publication of this method but did not find a reference in the manual or on the gromacs website. Can anybody tell me the publication o

Re: [gmx-users] Help to run demo- reg

2010-10-14 Thread Mark Abraham
On 14/10/2010 7:19 PM, Sathish wrote: Dear all, I have installed gromacs 4.5.1 in RHEL5.5 server. Then i was started to run demo but still its running ( more then 5 hrs). How long will take time to complete. Any other possible way is there to increase speed ? Anybody can help me? It's proba

Re: [gmx-users] Questions about REMD calculations

2010-10-14 Thread Mark Abraham
On 15/10/2010 2:54 AM, ABEL Stephane 175950 wrote: Dear all, I come back to you for several questions about the futures replica-exchange calculations that i would like to perform. The system of interest will contain 12 peptides (with 7 residues each) and 4 water molecules, it come from a

[gmx-users] Re: Re: Re: g_velacc problem (Florian Dommert)

2010-10-14 Thread Eudes Fileti
Dear Florian, thanks again. I have worked with confined systems, where motion in a given direction/plane is preferred. The accuracy of the MSD approach for calculating the diffusion coefficient has been questioned for this my system. So I need to calculate D via VACF. Considering my limited abiliti

Re: [gmx-users] Re: Extracting potential energy of protein units

2010-10-14 Thread Justin A. Lemkul
Jyoti Mahalik wrote: Message: 2 Date: Thu, 14 Oct 2010 21:56:22 +0200 From: David van der Spoel Subject: Re: [gmx-users] Extracting potential energy of protein units To: Discussion list for GROMACS users Message-ID: <4cb76066.8050...@xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-

[gmx-users] Re: Extracting potential energy of protein units

2010-10-14 Thread Jyoti Mahalik
Message: 2 Date: Thu, 14 Oct 2010 21:56:22 +0200 From: David van der Spoel Subject: Re: [gmx-users] Extracting potential energy of protein units To: Discussion list for GROMACS users Message-ID: <4cb76066.8050...@xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 201

[gmx-users] RE : Questions about REMD calcula tions

2010-10-14 Thread ABEL Stephane 175950
Dear all, Thank you very much Chris, Xavier and ms (;) for your comments and I will take into account your suggestions in my proposal (for GENCI, Chris ;)) . A bientot Stefane -- Message: 1 Date: Thu, 14 Oct 2010 17:22:

Re: [gmx-users] Extracting potential energy of protein units

2010-10-14 Thread David van der Spoel
On 2010-10-14 21.51, Jyoti Mahalik wrote: Using g_energy I can extract the energy of the whole system. But I want to extract the energy (potential energy) of the protein units in my system. Is it possible to do it in GROMACS or any other application? How would you define that? -- David van der

[gmx-users] Extracting potential energy of protein units

2010-10-14 Thread Jyoti Mahalik
Using g_energy I can extract the energy of the whole system. But I want to extract the energy (potential energy) of the protein units in my system. Is it possible to do it in GROMACS or any other application? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/l

Re: [gmx-users] Questions about REMD calculations

2010-10-14 Thread XAvier Periole
On Oct 14, 2010, at 11:42 AM, ms wrote: On 14/10/10 17:32, XAvier Periole wrote: Then I am not a fan of implicit solvents so I'll pass on that, then for the coarse grained FF the OPEP FF seem to be fine for your application. You can also look at the ones from Deserno's group (bereau-2009) a

Re: [gmx-users] Questions about REMD calculations

2010-10-14 Thread ms
On 14/10/10 17:32, XAvier Periole wrote: Then I am not a fan of implicit solvents so I'll pass on that, then for the coarse grained FF the OPEP FF seem to be fine for your application. You can also look at the ones from Deserno's group (bereau-2009) and from Feig's group (primo: gopal-2010). I a

Re: [gmx-users] Questions about REMD calculations

2010-10-14 Thread XAvier Periole
Well indeed the more atoms (degrees of freedom) in your system the more replicas you need to insure exchanges between temperatures ... I would say that even 135 replicas * 16 cpus= 2160 cpus ... that is still an enormous amount of cpu time for 12 small peptides :)) do you need to go up to 60

[gmx-users] partial pressure

2010-10-14 Thread Vitaly Chaban
Hi all, Is there a trick in gromacs to exclude some particles from the pressure calculation procedure? E.g. to get partial pressure(s)... Thank you! -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- gmx-users mailing li

[gmx-users] Questions about REMD calculations

2010-10-14 Thread chris . neale
Stefane, why are you hesitant to reduce the size of your system. If you can still address the same questions with a smaller system, then I'd say the answer is nearly always to use that smaller system (REMD or not). Besides, my gut feeling is that even if you had enough 271*16 cpus availab

[gmx-users] Questions about REMD calculations

2010-10-14 Thread ABEL Stephane 175950
Dear all, I come back to you for several questions about the futures replica-exchange calculations that i would like to perform. The system of interest will contain 12 peptides (with 7 residues each) and 4 water molecules, it come from a previous MD performed in NPT ensemble. With these s

Re: [gmx-users] Re: g_velacc problem (Florian Dommert)

2010-10-14 Thread Florian Dommert
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/14/2010 04:41 PM, Eudes Fileti wrote: > Dear Florian, thanks for the help. I wonder just one more thing. > Is it possible to obtain the lateral diffusion coefficient in a specific > plane (say xy) > using g_velacc? Or it is only possible with g

[gmx-users] Re: g_velacc problem (Florian Dommert)

2010-10-14 Thread Eudes Fileti
Dear Florian, thanks for the help. I wonder just one more thing. Is it possible to obtain the lateral diffusion coefficient in a specific plane (say xy) using g_velacc? Or it is only possible with g_msd? Bests eef ___ Eudes Eterno Fileti Física da Matéria Condens

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-14 Thread Sikandar Mashayak
hey thanks Sander for bringing my attention to -nt option.. ;) -- sikandar On Thu, Oct 14, 2010 at 6:08 AM, Sander Pronk wrote: > > On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote: > > > Recently I installed gromacs4.5.1 without mpi support on my workstation > with 8 cores using cmake and m

Re: [gmx-users] Martini parameters for monoolein

2010-10-14 Thread George Khelashvili
Dear Javier, Thank you for you suggestions. I am looking into these things and for sure take yours and Xavier's earlier comments into account. Sincerely, George On 10/14/2010 3:57 AM, Javier Cerezo wrote: Hello George. I would inspect PG lipid head (in Tieleman's website) in order to ext

[gmx-users] Is there a publication of the implemented reaction-field method?

2010-10-14 Thread Sascha Rehm
Dear all, to deal with my long-range interactions I used the reaction-field-zero method. Therefore I searched for a publication of this method but did not find a reference in the manual or on the gromacs website. Can anybody tell me the publication on which the implemented reaction-field is b

Re: [gmx-users] g_wham: "Pull geometry direction_periodic not supported"

2010-10-14 Thread Jochen Hub
On 9/18/10 Sep 18,10:17 PM, Jochen Hub wrote: On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote: Hi gmx-users I finished a series of pulling runs using the "periodic_direction" option and when I run the g_wham analysis I received the following message. ---

Re: [gmx-users] how to use gaff in gromacs

2010-10-14 Thread Justin A. Lemkul
fancy2012 wrote: Dear gmx users, In gromacs-4.5.1, we can use amber force field now, but if I want to gaff, a force field of small molecules, How should I do? Could someone give me some suggestion? If you have an AMBER topology, there are scripts on the GROMACS website to convert it to the

Re: [gmx-users] g_velacc problem

2010-10-14 Thread Florian Dommert
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/14/2010 01:33 PM, Eudes Fileti wrote: > Hi Florian, in fact I had already realized that it was possible > to calculate the VACF without using the -m option (although this option > was important for my calculations). > > I have not received any

[gmx-users] how to use gaff in gromacs

2010-10-14 Thread fancy2012
Dear gmx users, In gromacs-4.5.1, we can use amber force field now, but if I want to gaff, a force field of small molecules, How should I do? Could someone give me some suggestion? Thanks in advance! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

Re: [gmx-users] Re: the density of liquid benzene is too large

2010-10-14 Thread Justin A. Lemkul
Cenfeng Fu wrote: Several possible reasons: 1. The force field parameters aren't perfect, so there is some inherent disagreement between simulation and reality. What is the expected value for this force field? 2. You're using the isothermal compressibility for wat

Re: [gmx-users] Polar Hydrogen missing using PRODRG

2010-10-14 Thread Justin A. Lemkul
Jennifer Williams wrote: Hi, So, I did as suggested. Ran PRODRG the first time using the JME Editor and took the pdb file from this. Then I added the ADDHYD OAE underneath (actually it doesn't matter which O (OAD or OAE) is protonated as long as it is only one of them). The first bit of

Re: [gmx-users] Polar Hydrogen missing using PRODRG

2010-10-14 Thread Jennifer Williams
Hi, So, I did as suggested. Ran PRODRG the first time using the JME Editor and took the pdb file from this. Then I added the ADDHYD OAE underneath (actually it doesn't matter which O (OAD or OAE) is protonated as long as it is only one of them). The first bit of output looked encouraging

Re: [gmx-users] Please guide me

2010-10-14 Thread Justin A. Lemkul
mohsen ramezanpour wrote: I am not sure. How can I check it? I think as you.but I don't know what and how can I modify it. Look at the .log file for any indication of whether or not the job is still running. Check the .edr and .xtc files with gmxcheck to see how many frames they contain.

[gmx-users] g_velacc problem

2010-10-14 Thread Eudes Fileti
Hi Florian, in fact I had already realized that it was possible to calculate the VACF without using the -m option (although this option was important for my calculations). I have not received any attachment, have you send me something? If necessary, please, send it to my email. Following your sug

Re: [gmx-users] Please guide me

2010-10-14 Thread mohsen ramezanpour
ocourse my running took a few hours time.is it possible crashing? On Thu, Oct 14, 2010 at 2:54 PM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > I am not sure. > How can I check it? > I think as you.but I don't know what and how can I modify it. > > > On Thu, Oct 14, 2010 at 1:52 PM

Re: [gmx-users] Please guide me

2010-10-14 Thread mohsen ramezanpour
I am not sure. How can I check it? I think as you.but I don't know what and how can I modify it. On Thu, Oct 14, 2010 at 1:52 PM, ms wrote: > On 14/10/10 08:51, mohsen ramezanpour wrote: > >> Dear All >> >> I am running a seamulated anneaking + MD in my cluster. >> I had done it for 2 times. >>

Re: [gmx-users] Gromacs installation problem @ RHEL5.5 server

2010-10-14 Thread Sander Pronk
On 14 Oct 2010, at 05:49 , Sikandar Mashayak wrote: > Recently I installed gromacs4.5.1 without mpi support on my workstation with > 8 cores using cmake and make -j 8, make install commands ( as suggested on > installation instructions). > > Now when I do mdrun it automatically utilizes all t

Re: [gmx-users] Polar Hydrogen missing using PRODRG

2010-10-14 Thread Justin A. Lemkul
You need to run PRODRG twice. The first time, do not use ADDHYD. Make note of the atom names that PRODRG assigns. Then run PRODRG a second time, using ADDHYD with the atom name that PRODRG uses for the O atom you want protonated. -Justin Jennifer Williams wrote: Hi Justin, Thanks for

Re: [gmx-users] Polar Hydrogen missing using PRODRG

2010-10-14 Thread Jennifer Williams
Hi Justin, Thanks for your answer. The ADDHYD in the FAQ sounds like exactly what I need however I can't get this command to work. I draw in my molecule using the JME editor and get this .pdb file in the PRODRG window. CC(C)Cc1ccc(C(C)C(=O)O)cc1 JME 2002.05 Thu Oct 14 10:48:38 BST 2010

Re: [gmx-users] Please guide me

2010-10-14 Thread ms
On 14/10/10 08:51, mohsen ramezanpour wrote: Dear All I am running a seamulated anneaking + MD in my cluster. I had done it for 2 times. but my results are not as i expect. I have attached my md.mdp file for you,I don't know which part of it is wrong. what i like to result is to change tempretur

Re: [gmx-users] Percentage of H-bonds

2010-10-14 Thread Carla Jamous
Thank you Justin, you Perl script has been a great help! Cheers, Carla On Mon, Oct 11, 2010 at 4:31 PM, Justin A. Lemkul wrote: > > I wrote a Perl script to do a similar task (appended below). Perhaps it > will be useful to you. I hope it works; I had to hack out some things that > were spec

[gmx-users] Help to run demo- reg

2010-10-14 Thread Sathish
Dear all, I have installed gromacs 4.5.1 in RHEL5.5 server. Then i was started to run demo but still its running ( more then 5 hrs). How long will take time to complete. Any other possible way is there to increase speed ? Anybody can help me? Advance thanks -- -- Regards, N. Sathishkumar, -- gm

Re: [gmx-users] Martini parameters for monoolein

2010-10-14 Thread Javier Cerezo
Sorry, for the mistake: not Tieleman's website, but Martini's. POPG, is an example for PG lipid. In that one, the OH-C-C-OH is represented with a P4 particle as Xavier proposed. Javier El 14/10/10 09:57, Javier Cerezo escribió: Hello George. I would inspect PG lipid head (in Tieleman's webs

Re: [gmx-users] Martini parameters for monoolein

2010-10-14 Thread Javier Cerezo
Hello George. I would inspect PG lipid head (in Tieleman's website) in order to extract the parameters for some groups, such as the "glicero-ester" (atom name GL0 in the topology), and then take a particle for usually used for esters such as "Na". Anyway, even that topology for Tieleman is no

[gmx-users] Please guide me

2010-10-14 Thread mohsen ramezanpour
Dear All I am running a seamulated anneaking + MD in my cluster. I had done it for 2 times. but my results are not as i expect. I have attached my md.mdp file for you,I don't know which part of it is wrong. what i like to result is to change tempreture from 420 in 0 ps to 450 in 20 ps and then gra

Antw: [gmx-users] free energy decomposition

2010-10-14 Thread Emanuel Peter
Hi, I think the PMF is something like PMF = kT ln[g(r)] where g(r) is the radial distribution function from g_rdf. Emu >>> Sanku M 13.10.10 17.35 Uhr >>> Hi, I am studying Potential of mean force(PMF) of association of two peptides. I want to decompose the PMF into energy(enthalpy)