Re: [gmx-users] Re: How to read xtc file?

Hi Zhongqiao, Try to dig up a version of CONCOORD from Bert de Groot (source code). This contains xtc IO routines in fortran... Cheers, Tsjerk On 5/15/07, Yang Ye <[EMAIL PROTECTED]> wrote: You shall try link against libmd, and libgmx (-lmd -lgmx) On 5/15/2007 9:20 AM, Hu Zhongqiao wrote: >

Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat

Hi Nicolas, Have a look at the ff*bon.itp of your choice and go all the way to the bottom. You can see there how the connections are handled further for e.g. heme and can add the angles and dihedrals you want. Also, you report bonds between the zinc and a number of other atoms. This is probably

Re: [gmx-users] ci variable range error in parallel but NOT in serial

dtmirij wrote: Hello everyone, I am running starting from a minimized/equilibrated structure. When I run the the system with my serial built executable, it runs fine and the energies and pressures look fine. When I run the exact same system from the same starting conditions using my serial buil

Re: [gmx-users] about counterions

Rui Li wrote: Dear Mark Thank you for your reply Do you mean I can ignore the charge? Only if you want an expensive random number generator. If the topology is broken, what should I do? I already answered this. Appearing not to read the detailed reply that someone gave up their time to w

Re: [gmx-users] Ligand Parameters

David Mobley wrote: Justin, I have also considered submitting an analog of my compound to PRODRG (normal aromatic ring instead of one containing O+) to get the dihedrals, etc. and then re-calculating charges under ANTECHAMBER. Any thoughts on that approach? Presumably dihedrals, etc are af

Re: [gmx-users] Re: How to read xtc file?

You shall try link against libmd, and libgmx (-lmd -lgmx) On 5/15/2007 9:20 AM, Hu Zhongqiao wrote: >Install gromacs. Then check that $(GMXHOME)/lib/$(CPU)/libxtfc.whatever >exists. >Mark Dear Mark, The gmx has been installed in our cluster. But I can not find any files related to libxtfc

Re: [gmx-users] about counterions

Dear Mark Thank you for your reply Do you mean I can ignore the charge? If the topology is broken, what should I do? ÔÚÄúµÄÀ´ÐÅÖÐÔø¾­Ìáµ½: >From: Mark Abraham <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] abou

[gmx-users] Re: How to read xtc file?

>Install gromacs. Then check that $(GMXHOME)/lib/$(CPU)/libxtfc.whatever >exists. >Mark Dear Mark, The gmx has been installed in our cluster. But I can not find any files related to libxtfc under /lib. That means something is lost during the installation, right? In this case, are there any ot

RE: [gmx-users] energy minimization of POPC crash

>and why the em crash? Posting here what command line you used, the contents of the .mpd file and what the error output was would be a great start to people being able to answer that question. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian Co

Re: [gmx-users] Ligand Parameters

David, Thank you for the quick and detailed reply. I thought that the analog approach would be a bit too quick-and-dirty, anyway :-) I will set to work on making some new parameters based on the information you've provided, and I will likely focus on compatibility with the GROMOS force fields.

Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat

Sorry, the message has been sent too fast, the 4 bonds have been correctly created now. So, the correct specbond line is: CYS SG 1 ZN2 ZN 1 0.25 CYSZZN There is still an angles that lacks (the S-ZN-S angle), but I can add it manually. Nicolas Sorry for t

Re: [gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat

Thnaks for your answer, I have solved the problem with the lacking CD1 atom. There was a weid end of line the line jus before. But pdb2gmx is still unable to link correctly the ZN2 residue with the 4 CYS. The distance between SG and ZN atoms are computed correctly (I have the bon lenght to 0.2

[gmx-users] protein in popc

It's probably easiest to do by hand, but here's a script anyway: #!/bin/bash a=wc -l protein.gro b=$(expr $a + 1) head -n "$b" protein.gro > first.gro c=wc -l bilayer.gro d=$(expr $c - 2) tail -n "$d" bilayer.gro > last.gro cat first.gro last.gro > total.gro n=wc -l total.gro o=$(expr $n - 3) p=

Re: [gmx-users] Ligand Parameters

Justin, I am interested in simulating some small molecules that involve oxygen in aromatic rings (which thus bears a +1 charge). I tried to submit one of these molecules to PRODRG, but got an error indicating that there were too many bonds to O. I thought this issue might arise, due to the unu

[gmx-users] turning off output of dgdl.xvg and VCM messages?

All, I'm trying to set up some storage-limited calculations. Two related questions: (1) Is there a way to prevent dgdl.xvg from being written in free energy calculations? (2) Is there a way to prevent messages relating to COM removal from being written to the log file? For example, I get stuff l

[gmx-users] Ligand Parameters

Hello all, I am interested in simulating some small molecules that involve oxygen in aromatic rings (which thus bears a +1 charge). I tried to submit one of these molecules to PRODRG, but got an error indicating that there were too many bonds to O. I thought this issue might arise, due to the un

[gmx-users] ci variable range error in parallel but NOT in serial

Hello everyone, I am running starting from a minimized/equilibrated structure. When I run the the system with my serial built executable, it runs fine and the energies and pressures look fine. When I run the exact same system from the same starting conditions using my serial built executable on t

Re: [gmx-users] TREMD in development version

N-J.M. Macaluso wrote: Hi, I have a question regarding the implementation of temperature replica exchange MD (TREMD) in the development version of Gromacs. Is it possible to simulate more than one replica on one processor? As far as I know, the distributed version 3.3 can only accept one r

[gmx-users] TREMD in development version

Hi, I have a question regarding the implementation of temperature replica exchange MD (TREMD) in the development version of Gromacs. Is it possible to simulate more than one replica on one processor? As far as I know, the distributed version 3.3 can only accept one replica per processor.

Re: [gmx-users] How to read xtc file?

Hu Zhongqiao wrote: Hi, I have been thinking how to write a Fortran program to read xtc file for a long time. The gmx homepage provides a code testxtc. But when I simply compile it, some errors are shown as follows: /tmp/ifortuDk9ZY.o(.text+0x5c): In function `MAIN__': : undefined referen

[gmx-users] How to read xtc file?

Hi, I have been thinking how to write a Fortran program to read xtc file for a long time. The gmx homepage provides a code testxtc. But when I simply compile it, some errors are shown as follows: /tmp/ifortuDk9ZY.o(.text+0x5c): In function `MAIN__': : undefined reference to `xdrfopen_' /tmp/i

Re: [gmx-users] about counterions

Rui Li wrote: Dear all, I am new to gmx. When I run grompp, it prompt: System has non-zero total charge: 1.172000e+01 The number isn't integer, So how many counterions I should add? Never mind about ions, probably your topology is broken before you got started :-) Check your capping groups. I

[gmx-users] about counterions

Dear all, I am new to gmx. When I run grompp, it prompt: System has non-zero total charge: 1.172000e+01 The number isn't integer, So how many counterions I should add? Any reply is appreciated. ___ gmx-users mailing listgmx-users@gromacs.org http:/

[gmx-users] protein in popc

Dear all I have made a hole in POPC128a bilayer(make_hole).how can i insert protein into the hole? thanks Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ _