[gmx-users] trjcat error

Dear all , I did a simulation for 2 ns then i extanded the simulation using tpbconv for another 2 ns. After that, I tried to combine the two trajectory files by using trjcat by using the following command: trjcat -f md1.xtc extend1.xtc -o combine.xtc but it showed a warning that it couldn't

[gmx-users] (no subject)

Justin A. Lemkul wrote: [EMAIL PROTECTED] wrote: Hi everyone, I'm having problems running an md simulation (with gmx-4.0.2) using vsites and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem seems to occur when the molecule crosses pbc, since the first sign of the

Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

--- Missatge original Assumpte: De: [EMAIL PROTECTED] Data: Tue, Novembre 25, 2008 9:52 am A:Discussion list for GROMACS users gmx-users@gromacs.org [EMAIL PROTECTED]

[gmx-users] how many pairs are exchanged in replica exchange

  Hi, I am new to Replica exchange molecular dynamics. I obtained the optimal temperature distribution based on the lowest and highest tempearture and exchange probability from the REMD caclulator , available through the gromacs homepage. There were 17 temperaure values as output. I

Re: [gmx-users] trjcat error

Hi QIU YI HUAN, Was it a warning or did it exit without producing output? Please be more complete in your postings. Maybe a good idea to include the output of the program? In case of an error use gmxcheck first on each of the trajectories. It seems that one of them is giving an error. Then, if

Re: [gmx-users] coarse grain in gromacs

On Mon, 24 Nov 2008 22:28:36 -0500 Justin A. Lemkul [EMAIL PROTECTED] wrote: BIN ZHANG wrote: Hi,: Is it possible to solvate the system using coarse grained water molecule? I tried command: genbox -cp cg_protein.pdb -cs cgwat.pdb -o cg_protein_water.pdb, but get Segmentation

[gmx-users] trjcat problems

Dear all, After trjcat, I wish to view the combined trajactory using ngmx. The problem is, how can i get the tpr combined file in oder to view the trajectory using ngmx? thanks for the help QIU YI HUAN DEPARTMENT OF CHEMISTRY, FACULTY OF SCIENCE, UNIVERSITY PUTRA MALAYSIA, MALAYSIA.

[gmx-users] Loss of bonds in HEME iron after pdb2gmx

Hello, I am working with the simulation of cytochromeP450. In the output of the pdb2gmx command, the iron atom in the HEME loses all the bonds, including the sulphide bond with cystine. Also, the command changed the residue name from HEME to HEC. During the execution of the pdb2gmx, I get this

[gmx-users] DPPC simulations

Hi all when i run grompp but it gives Atomtype LC3 not found Could anyone explain me briefly? Jenny Hsu -- Jenny Hsu, Biotechnology Dept., Ming Chuan University, Taiwan, R.O.C ___ gmx-users mailing list

[gmx-users] Re: gmx-users Digest, Vol 55, Issue 130

/attachments/20081125/1b326dcb/attachment-0001.html -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

[gmx-users] location of specbond.dat-solved

Hello, The file in the local directory is the one that is considered. I am sorry for the previous mail. Regards, Sarada Graduate student, NCBS, Bangalore. Hello, I am working in a cluster environment and so, all files there including specbond.dat file are write protected. Can someone indicate

[gmx-users] location of specbond.dat

Hello, I am working in a cluster environment and so, all files there including specbond.dat file are write protected. Can someone indicate how I can specify that the program must consider the modified file (specbond.dat) in my local working directory rather than the one in the main directory?

Re: [gmx-users] DPPC simulations

Dear Justin: I try to include lipid.itp into ffgmxnb.itp and I also tried to add the different sections [ atomtypes ], [ pairtypes ], etc... of the lipid.itp files to ffgmx* files but when i run grompp, i got another fetal error Atomtype 'C' not found Jenny 2008/11/25 Justin A. Lemkul [EMAIL

Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx

[EMAIL PROTECTED] wrote: Hello, Sorry, I realised the HEME HEC naming was not the problem. But still the pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets protonated and doesnot form a bond with HEME. I tried to preserve the bonds by editing the specbond.dat file. I do not

Re: [gmx-users] DPPC simulations

Jenny Hsu wrote: Dear Justin: I try to include lipid.itp into ffgmxnb.itp and I also tried to add the different sections [ atomtypes ], [ pairtypes ], etc... of the lipid.itp files to ffgmx* files All you should have to do is copy all the sections of lipid.itp into ffgmxnb.itp, with the

[gmx-users] Extracting the water molecules in hydration layer

Dear all, is there an easy way to extract only the water molecules in the hydration layer/shell around the protein/polymer chain? I need them both for visualization of the trajectory and some analysis. I can do this by writing my own program alright, but I wanted to know if there is any in-built

Re: [gmx-users] Extracting the water molecules in hydration layer

On Tue, 25 Nov 2008 20:39:37 +0530 Suman Chakrabarty [EMAIL PROTECTED] wrote: Dear all, is there an easy way to extract only the water molecules in the hydration layer/shell around the protein/polymer chain? I need them both for visualization of the trajectory and some analysis. trjorder

[gmx-users] course grain model for DNA

Hi all users, when I am using the gromacs to simulate the course grain model for DNA, it seems that the software doesn't recognize my force field file. I have included all the bond and non-bond parameters in the bon.itp and nb.itp file. During my simulation , I found that the base pair for C-G

[gmx-users] Re: how to show dodecahedron box in VMD

Dear all: I am trying to show the dodecahedron box only in vmd since my simulation box is dodecahedron. If I include water, I can see the box is dodecahedron. But I want to get rid off all of water, then my box will not appear there. How can I keep the dodecahedron box boundaries and solute

[gmx-users] TYR residue in OPLS-AA

I think that it is worth having a central repository that lists modifications to forcefield files during development -- especially changes as opposed to simple additions. It's not always a huge deal, but it would be nice if this information was easily available. Revision history might be one

Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

Hi everyone, As I wrote yesterday, I'm having problems running stable simulations with vsites and constraints in all bonds in different time-steps using gmx-4.0.2. As long as the dna strand does not cross pbc, the simulations run fine (the longest I did was 5ns). The dna topology was generated

[gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

When two spaces are included the #define KEYWORD is incompletely removed from the file. In case my conclusion about the exact nature of the error is incorrect, here is more information. I have a ffcharmbon.itp file that contains: [ dihedraltypes ] #define improper_NC2_X_X_C_ 180.0

RE: [gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

Hi, That is an annoying bug. I fixed it for 4.0.3. If you want it fixed now, the diff is below. Berk RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v retrieving revision 1.9 diff -r1.9 gmxcpp.c 121,122c121,122 sscanf(define,%s,name); ptr = define + strlen(name); ---

Re: [gmx-users] course grain model for DNA

He, Yang wrote: Hi all users, when I am using the gromacs to simulate the course grain model for DNA, it seems that the software doesn't recognize my force field file. I have included all the bond and non-bond parameters in the bon.itp and nb.itp file. During my simulation , I found that

Re: [gmx-users] course grain model for DNA

If there is fraying at the edges only, you can impose distance restraints on some of the hydrogen bonds at the ends. You need to modify md.mdp to turn on distance restraints and have a new file called disres.itp that mentions the distances to be restrained. Hope this helps, Mrinalini On Wed,

Re: [gmx-users] how many pairs are exchanged in replica exchange

sarbani chattopadhyay wrote: Hi, I am new to Replica exchange molecular dynamics. I obtained the optimal temperature distribution based on the lowest and highest tempearture and exchange probability from the REMD caclulator , available through the gromacs homepage. There were 17

[gmx-users] correct processing of #define statements by grompp in gromacs 4.0.2 requires exactly one space after #define

Nice trick with %n on sscanf. I went with the manual replacement but I do appreciate learning new things, thanks Berk, Chris. ### Hi, That is an annoying bug. I fixed it for 4.0.3. If you want it fixed now, the diff is below. Berk RCS file: /home/gmx/cvs/gmx/src/kernel/gmxcpp.c,v

[gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

Hi Justin, Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said the topology file does contain the bonds and I need not have made the modificatins to specbond.dat. But using the original specbond.dat does not prevent the protonation of CYS. I renamed CYS as CYS2 in the input

[gmx-users] Using double precision files with single precision version

Hi All, I had a few MD runs with double precision in gromacs, Can I use single precision version of gromacs to play with those files e.g making movie files and extracting h_bond information. I am afraid if it will affect my results. Please suggest With thanks, Vivek