[gmx-users] How to change the resname?

Hello, first, I make a grateful acknowledgement for Mark and Justin's help to guide me to install the gromacs,I have installed it well. I have another question need you help , could I change the resname in the .gro and .top or .itp documents? if yes, how shall I do, just change it ?   Thank you

[gmx-users] Re: charmm lipid simulation and vsites

Hello David, I send answer to the gromacs mailing list also. 12 apr 2010 kl. 17.51 skrev David Caplan: > I am still experimenting with the CHARMM27 support in Gromacs. I am > using a very recent git version (from last week). > > Currently, I'm trying to equilibrate a membrane bilayer with virtua

Re: [gmx-users] Amino acid simulation

Thanks Justin. It worked perfectly. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Apr 13, 2010 at 1:08 AM, Justin A. Lemkul wrote: > > > Chandan Choudhury wrote: > >> Hello gmx-users >> >> I am trying to simulate an amino acid (say GLN). It can be as a >> zwitterionic form or unc

[gmx-users] Segmentation fault with g_order

Hello I tried to run g_order on a cluster with Core 2 Quad Q6600 processor where the Gromacs Suite 4.0.1 has been compiled in single precision. The program stops with a message from the compiler (i.e. in Spanish): "Violación de segmento" (=Segmentation fault, I guess) and I couldn't find an a

[gmx-users] How to prepare the two tolopogy files when doing TI calculation?

Dear GMX users, I want to do some TI calculation using GMX, and I have learned the tutorial of TI calculation from this web site http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. So I have know how to run TI calculations. But there is still a problem. I don't know how to

[gmx-users] Re: Regarding Error "Atomtype OS not found"

> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp > Generated 837 of the 2346 non-bonded parameter combinations > --- > Program grompp, VERSION 4.0.5 > Source code file: toppush.c, line: 947 > Fatal error: > Atomtype OS not fo

Re: [gmx-users] Segmentation fault with g_order

Javier Cerezo wrote: Hello I tried to run g_order on a cluster with Core 2 Quad Q6600 processor where the Gromacs Suite 4.0.1 has been compiled in single precision. The program stops with a message from the compiler (i.e. in Spanish): "Violación de segmento" (=Segmentation fault, I guess) a

Re: [gmx-users] How to change the resname?

kecy...@sina.com wrote: Hello, first, I make a grateful acknowledgement for Mark and Justin's help to guide me to install the gromacs,I have installed it well. I have another question need you help , could I change the resname in the .gro and .top or .itp documents? if yes, how shall I do, ju

[gmx-users] Fwd: small help

Dear Satish, you'll find more help in the mailing list of GROMACS. regarding the use of g_rmsdist, the option -h is very useful ... you can access single residues or subpart of a system by using and index. XAvier. Begin forwarded message: From: satish kumar ainala Date: April 13, 2010 12:1

Re: [gmx-users] Re: Regarding Error "Atomtype OS not found"

Vitaly V. Chaban wrote: Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 837 of the 2346 non-bonded parameter combinations --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 947 Fatal error: Atom

[gmx-users] g_sas to calculate the n-hexane/water interface surface area

Hi all, I have a question regarding the g_sas command. Let's say I have an n-hexane/water interface. I want to calculate the accessible area between these two media. If I were to choose the calculation group as the 'system', and the output group as 'hexane' then, it should give me that area? Rega

Re: [gmx-users] How to prepare the two tolopogy files when doing TI calculation?

On 13/04/2010 7:35 PM, fancy2012 wrote: Dear GMX users, I want to do some TI calculation using GMX, and I have learned the tutorial of TI calculation from this web site http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial. So I have know how to run TI calculations. But there i

[gmx-users] OpenMM

Hi all, I'm using the Application Programming Interface openMM for executing molecular dynamics simulations with Gromacs on an NVIDIA GTX 295 GPU (here is installed CUDA SDK for issuing and managing computations on GPU). Even if I have followed all the instructions reported for the correct i

[gmx-users] Re: Regarding Error "Atom type OS not found"

Dear Mark, I have used following .top file. ; Include forcefield parameters #include "ffG53a6.itp" #include "drg.itp" [ moleculetype ] ; Namenrexcl Protein_X 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1

Re: [gmx-users] Re: Regarding Error "Atom type OS not found"

Jignesh Patel wrote: Dear Mark, I have used following .top file. ; Include forcefield parameters #include "ffG53a6.itp" #include "drg.itp" Let me guess, drg.itp is from PRODRG? Then you probably have ffgmx atom types (like "OS") that are not supported by G53a6. Thus you are mixing force

Re: [gmx-users] OpenMM

Hi,O On 04/13/2010 04:23 PM, PACIELLO GIULIA wrote: Even if I have followed all the instructions reported for the correct installation of GPU, CUDA, OpenMM and even if my .mdp file for the simulation is written following the features supported in the release Gromacs-OpenMM, the output of the s

[gmx-users] combining energy files

Hello, I am a running a simulation of 100ns, so I have two edr files md.edr and md.part0002.edr. When I calculate some of the energy values using g_energy for each of the .edr files individually I get the following result: For md.edr: Statistics over 27120401 steps [ 0. thru 54240.8

[gmx-users] Question about setting deprotonated cys in enzyme structure ....

Dear all I am preparing the topology for my enzyme molecule using pdb2gmx tool. But first of all, I run a PROPKA program in order to assign the correct protonation state for my molecule. As a result of this calculation I obtained a pair of cysteines which should be deprotonated at pH 7 (f

Re: [gmx-users] Question about setting deprotonated cys in enzyme structure ....

Alberto Sergio Garay wrote: Dear all I am preparing the topology for my enzyme molecule using pdb2gmx tool. But first of all, I run a PROPKA program in order to assign the correct protonation state for my molecule. As a result of this calculation I obtained a pair of cysteines which should

Re: [gmx-users] combining energy files

That looks like a nice bug! You should specify which gmx version you are using. That would help getting it fixed. On Apr 13, 2010, at 21:34, nishap.pa...@utoronto.ca wrote: Hello, I am a running a simulation of 100ns, so I have two edr files md.edr and md.part0002.edr. When I calculate

Re: [gmx-users] Question about setting deprotonated cys in enzyme structure ....

On Apr 13, 2010, at 21:23, Alberto Sergio Garay wrote: Dear all I am preparing the topology for my enzyme molecule using pdb2gmx tool. But first of all, I run a PROPKA program in order to assign the correct protonation state for my molecule. As a result of this calculation I obtaine

Re: [gmx-users] combining energy files

I am using gromacs-4.0.5. Thanks. Quoting XAvier Periole : That looks like a nice bug! You should specify which gmx version you are using. That would help getting it fixed. On Apr 13, 2010, at 21:34, nishap.pa...@utoronto.ca wrote: Hello, I am a running a simulation of 100ns, so I have

Re: [gmx-users] combining energy files

nishap.pa...@utoronto.ca wrote: I am using gromacs-4.0.5. Try upgrading to the newest version (4.0.7), and if that does not fix the problem, please report back with the exact command line, gmxcheck output (on the .edr file), compilers used, hardware, etc. -Justin Thanks. Quoting XAv

[gmx-users] Re: How to prepare the two tolopogy files when doing TI calculation?

Dear Mark, I know that the tutorial can go through, my problem is just how to generate the two topology files. From the tutorial, I know how to run TI calculation, but first, I got to know how to prepare these files, both for topology and coordinate files. I will highly appreciate for your sugg

Re: [gmx-users] Re: How to prepare the two tolopogy files when doing TI calculation?

fancy2012 wrote: Dear Mark, I know that the tutorial can go through, my problem is just how to generate the two topology files. From the tutorial, I know how to run TI calculation, but first, I got to know how to prepare these files, both for topology and coordinate files. I will highly app

[gmx-users] questions about energy minimization

To whom may be concerned, I am just doing an energy minimization on a polymer chain ---PVA, which contains 50 repeat units. I am puzzled about how to choose an appropriate emtol. It's said to be a maximum force in the system. But how to make sure that the emtol I choose is big or small enoug

Re: [gmx-users] questions about energy minimization

On 14/04/2010 1:28 PM, DreamCatcher wrote: To whom may be concerned, I am just doing an energy minimization on a polymer chain ---PVA, which contains 50 repeat units. I am puzzled about how to choose an appropriate emtol. It's said to be a maximum force in the system. But how to make sure

Re: [gmx-users] OpenMM

Hi, thanks a lot for your answer, but I have some doubts yet... My .gro files are very different and I'm not sure that the architecture (CPU / GPU) could influence the result so much as in my example (the first is the output of the serial code and the second that of the parallel ones). SERIA

Re: [gmx-users] OpenMM

On 14/04/2010 4:31 PM, PACIELLO GIULIA wrote: Hi, thanks a lot for your answer, but I have some doubts yet... My .gro files are very different and I'm not sure that the architecture (CPU / GPU) could influence the result so much as in my example (the first is the output of the serial code and the

Re: [gmx-users] OpenMM

Ok...so how could I know the energies among atoms? And how can I test if my parallel code is running in the correct manner? Thanks, Giulia On Wed, 14 Apr 2010 16:43:13 +1000 Mark Abraham wrote: On 14/04/2010 4:31 PM, PACIELLO GIULIA wrote: Hi, thanks a lot for your answer, but I have some d

Re: [gmx-users] OpenMM

On 14/04/2010 4:52 PM, PACIELLO GIULIA wrote: Ok...so how could I know the energies among atoms? Since it's not reported, you can't get breakdowns of energies. That's a limitation from the use of GPU. If you want this information, perhaps do your simulation on the GPU and re-rerun selected fr