RE: [gmx-users] (no subject)

Hi Jeremy, I am not an expert of amber ff, but what I have notice form the ffbonded.itp file of amber99sb is that it does not have an improper header and it might use dihedraltypes for both proper and improper; or constratinttypes. It would be good to get a comment from someone who knows how am

[gmx-users] (no subject)

Dear EB, Many thanks for the kind reply! We have revised the improper section followed your advice. The force field is amber99sb. Unfortunately, the program complained again, "No default proper dih. types'. Any advice? Thanks! Cheers Jeremy --- Hi Jeremy, I have checked how impro

[gmx-users] errors when using g_membed tool

Dear All, I carry out inserting a protein into lipid membrane by using g_membed tool. But i have errors : Fatal error: (i) Something is wrong with your membrane. Max and min z values are 12.15 and 0.01. (ii) Maybe your membrane is not centered in the box, but located at the box edge in

Re: [gmx-users] Is there any fundamental difference between the output of serial, gpu and parallel gromacs run

By the way we have used same gromacs version and also tried with other additional version. Sent from my iPhone On Mar 24, 2013, at 6:48 PM, Mark Abraham wrote: > In principle, you should be able to reproduce their results if you use the > same GROMACS version and the same algorithm. I would ch

Re: [gmx-users] Is there any fundamental difference between the output of serial, gpu and parallel gromacs run

We are using the same .mdp input file as they are provided in the Martini website. We don't understand what is wrong with us. However, we are trying to contact them. Once again thanks for your reply. Sent from my iPhone On Mar 24, 2013, at 6:48 PM, Mark Abraham wrote: > In principle, you sh

Re: [gmx-users] Is there any fundamental difference between the output of serial, gpu and parallel gromacs run

In principle, you should be able to reproduce their results if you use the same GROMACS version and the same algorithm. I would check very carefully that I have been using the same algorithm parameters - e.g. contact the authors to see if their .mdp files are available. On Sun, Mar 24, 2013 at 9:4

Re: [gmx-users] Format of .trr file

On Sun, Mar 24, 2013 at 9:59 PM, sudipta wrote: > Hi, > > Thanks for your reply. Forget about C/Fortran. Can I read it by some > advanced scripting languages such as python or matlab or JAVA without using > any gromacs tool. Is it possible? Yes. You were given a link already. There are other op

Re: [gmx-users] Format of .trr file

Hi, Thanks for your reply. Forget about C/Fortran. Can I read it by some advanced scripting languages such as python or matlab or JAVA without using any gromacs tool. Is it possible? We notice that there is a big precision difference between .xtc and .trr which affects drastically on the analysis

[gmx-users] Is there any fundamental difference between the output of serial, gpu and parallel gromacs run

Hi All, We were trying to test a simple lipid bilayer system using gromacs with martini model and polarizable CG water to validate the model. We have tested it by several ways such as varying gromacs version, precision, different platform, different initial configuration, increasing length of tra

Re: [gmx-users] Re: gro does not match top

Thanks! I did! :-) Sincerely, Shima From: Mark Abraham To: Discussion list for GROMACS users Cc: Shima Arasteh Sent: Sunday, March 24, 2013 9:50 PM Subject: Re: [gmx-users] Re: gro does not match top On Sun, Mar 24, 2013 at 2:32 PM, Justin Lemkul w

Re: [gmx-users] Re: gro does not match top

On Sun, Mar 24, 2013 at 2:32 PM, Justin Lemkul wrote: > > > On 3/24/13 9:02 AM, Shima Arasteh wrote: > >> In fact the genion does not add the neutralizing CL ions to gro file! Why? >> How can I solve this problem? >> >> > Using -nn and -conc is probably incompatible, because -conc will add some >

Re: [gmx-users] Format of .trr file

On Sun, Mar 24, 2013 at 3:35 PM, sudipta wrote: > Hi, > > Thank you very much for your reply. I appreciate your answer. However, if I > wish to read that file using C/Fortran interface then which C routine > should be convenient. There are several options. I found another > tool*gmxdump > * which

Re: [gmx-users] Format of .trr file

Hi, Thank you very much for your reply. I appreciate your answer. However, if I wish to read that file using C/Fortran interface then which C routine should be convenient. There are several options. I found another tool*gmxdump * which basically read the .trr file and gives the output. Can I link

Re: [gmx-users] Re: gro does not match top

On 3/24/13 9:02 AM, Shima Arasteh wrote: In fact the genion does not add the neutralizing CL ions to gro file! Why? How can I solve this problem? Using -nn and -conc is probably incompatible, because -conc will add some number of ions, which may not play nicely with the fact that you are th

[gmx-users] Re: gro does not match top

In fact the genion does not add the neutralizing CL ions to gro file! Why? How can I solve this problem?  Would you please help me? Sincerely, Shima - Original Message - From: Shima Arasteh To: Discussion list for GROMACS users Cc: Sent: Sunday, March 24, 2013 5:16 PM Subject: gro d

[gmx-users] gro does not match top

Hi, I am solving a protein in water. This protein has a charge of +3. After solvation there is 3272 water molecules. Next, I use genion command to add NACL 1M and 3 extra CL ions to neutralize the system. #genion -s ions.tpr -o cyclic_solv_ions.gro -p topol.top -nname CL -nn 3 -conc 1 After t

[gmx-users] how to convert Coarse Grained protein structure to all-atom structure

Dear gromacs users: I finished a coarse grained MD of a protein, but i cannot convert the coarse grained structure into all-atom structure, can anybody give me some advice on that? Best wishes Fugui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] helitr...@126.com

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Re: [gmx-users] How to specify water molecules number added to box?

- maxsol Cheers, EB On 24/03/2013, at 7:24 PM, "ca...@mail.ustc.edu.cn" wrote: > Dear all, > > I am new to gromacs. I would like to add water molecules of specific number > into my systems. As I found no answer out of the manual, I have to ask you > for help. How can I specify water molecul

Re: [gmx-users] A problem of adding new bond parameters

On Sun, Mar 24, 2013 at 6:42 AM, spin wrote: > Hello, everyone, > I have tried to create a mutant of CYS, the CYC, which the S was > replaced with a C at the end of its side chain. After using pdb2gmx to > build > the .top file, I added bond and nonbond parameters to link the side chain > of

Re: [gmx-users] How to specify water molecules number added to box?

On 2013-03-24 09:23, ca...@mail.ustc.edu.cn wrote: Dear all, I am new to gromacs. I would like to add water molecules of specific number into my systems. As I found no answer out of the manual, I have to ask you for help. How can I specify water molecules number (like 484 water molecules) adde

[gmx-users] How to specify water molecules number added to box?

Dear all, I am new to gromacs. I would like to add water molecules of specific number into my systems. As I found no answer out of the manual, I have to ask you for help. How can I specify water molecules number (like 484 water molecules) added into my system. Does it has anything with "-ci" an