[gmx-users] energy_extract

Dear Users ! I have took a penta peptide and did topology generation , I have solvated it with water box , now i did a minimization with zero step , to know the energy of the initial molecule , i used g_energy for the out put , like $ g_energy -f em.edr it gives as follows , i have to

Re: [gmx-users] micelle clustering

Thanks Mark, I will do the analysis in 4.5.4. Hope while doing the micelle clustering I will not get into a infinite loop as in 4.0.7. If I understand correctly, While using trjconv -pbc cluster, I should use -e 0.002 or the frames (-dump option) in the xtc file (generated after the micelles are

Re: [gmx-users] micelle clustering

On 1/07/2011 3:35 PM, sulatha M. S wrote: Hi Tsjerk, I installed gromacs myself. I put the modified gmx_trjconv.c code in the /src/tools subdirectory where the source code is located and tried the command make trjconv But it gives me a series of error messages, as given below. They're all m

Re: [gmx-users] micelle clustering

Hi Tsjerk, I installed gromacs myself. I put the modified gmx_trjconv.c code in the /src/tools subdirectory where the source code is located and tried the command make trjconv But it gives me a series of error messages, as given below. My gromacs version is 4.0.7. I would like to continue in this

Re: [gmx-users] Re: local pressure v4.5 issues

I downloaded v4.5 and v4.0 from the same websites as you mentioned in previous email. I am not sure why v4.5 give inconsistent results. I haven't try v4.0, because my simulation is using CHARMM FF. Could you give more details of conversion tpr files from v4.5 to v4.0 using CHARMM FF? Thank you v

Re: [gmx-users] Re: local pressure v4.5 issues

On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li wrote: > Hi Amit, > > I also encountered the same problem you mentioned. > In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one > file "localpressure.dat0". I tested first several frames of a trajectory, > the calculated pressure is n

Re: [gmx-users] Re: local pressure v4.5 issues

Hi Amit, I also encountered the same problem you mentioned. In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one file "localpressure.dat0". I tested first several frames of a trajectory, the calculated pressure is not the average of the pressure of individual frames. Btw,

Re: [gmx-users] Re: local pressure v4.5 issues

Hello Everyone, The git version of local pressure calculation at http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure is broken. I could not get it to work for my simulations. I installed gromacs local pressure version 4.0 from ftp://ftp.gromacs.org/pub/tmp/ I used

[gmx-users] g_velacc

Hello, I am trying to calcualte the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not geting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize

Re: [gmx-users] terminal_fixing

balaji nagarajan wrote: Dear Users ! i have tried in generating the -ter option in generating the topology file ! it asks the below if i give the ter option , Select start terminus type for TYR-1 0: NH3+ 1: ZWITTERION_NH3+ 2: NH2 3: None then if i give option 1 it chooses ZWITTERION

[gmx-users] terminal_fixing

Dear Users ! i have tried in generating the -ter option in generating the topology file ! it asks the below if i give the ter option , Select start terminus type for TYR-1 0: NH3+ 1: ZWITTERION_NH3+ 2: NH2 3: None then if i give option 1 it chooses ZWITTERION_NH3+ , i want to make the

Re: [gmx-users] rerun confusion

On 1/07/2011 1:57 AM, SebastianWaltz wrote: Hallo all together, I am working on a system of a small peptide solvated in CHCl3. I want to obtain the forces on the peptide atoms induced by the solvent. For this I used the rerun option of mdrun_d. I did it now in two ways: 1st: using trjconv to ge

[gmx-users] g_velacc

Hello, I am trying to calcualte the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not geting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize

Re: [gmx-users] Calculate distance between two atoms

Amjad Farooq wrote: Hello everyone, I would like to calculate distance between two atoms from an MD run. For example, how do I probe changes in distance between CD atom of Pro23 and OE1 atom of Glu75 as a function of simulation time. From the manual, I understand that one should use the c

Re: [gmx-users] Installation of gromacs-gpu on windows

Dear Andrew, Compiling on Windows was tested only using MSVC and I have no idea if it works or not under cygwin. You should just try, both cmake and gcc is available for cygwin so you might be lucky and get mdrun-gpu compiled without any additional effort. All binaries on the Gromacs webpage _are

[gmx-users] Calculate distance between two atoms

Hello everyone, I would like to calculate distance between two atoms from an MD run. For example, how do I probe changes in distance between CD atom of Pro23 and OE1 atom of Glu75 as a function of simulation time. From the manual, I understand that one should use the command g_dist that includ

Re: [gmx-users] pdb2gmx

Hi Simon, pdb2gmx takesthe first structure. Taking an average would ba awkward, as it is unlikely to correspond to a real structure. Cheers, Tsjerk On Jun 30, 2011 6:02 PM, "simon sham" wrote: Hi, I have a question about pdb2gmx. If a pdb file contains a multiple structures, will it average t

[gmx-users] pdb2gmx

Hi, I have a question about pdb2gmx. If a pdb file contains a multiple structures, will it average the coordinates or just pick one of the structures to convert? Thanks for your insight. Simon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] rerun confusion

Hallo all together, I am working on a system of a small peptide solvated in CHCl3. I want to obtain the forces on the peptide atoms induced by the solvent. For this I used the rerun option of mdrun_d. I did it now in two ways: 1st: using trjconv to get the pure peptide trajectory. When using the

Re: [gmx-users] Regarding PDB file

Ravi Kumar Venkatraman wrote: Dear All, To remove water of crystallization from pdb files. I removed following things from pdb file. REMARK 3 SOLVENT ATOMS: 78 . ..

[gmx-users] Regarding PDB file

Dear All, To remove water of crystallization from pdb files. I removed following things from pdb file. REMARK 3 SOLVENT ATOMS: 78 . . HETATM 1072

Re: [gmx-users] the effect of the ligand on each residue

ahmet yıldırım wrote: Dear Justin, Thanks for your reply. Well, to explore the effect of the ligand on protein g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg Select a group: 1 Selected 1: 'Protein' Select a group: 13 Selected 13: 'LİGAND' Does this choice make sense? Whet

Re: [gmx-users] the effect of the ligand on each residue

Dear Justin, Thanks for your reply. Well, to explore the effect of the ligand on protein g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg Select a group: 1 Selected 1: 'Protein' Select a group: 13 Selected 13: 'LİGAND' Does this choice make sense? 30 Haziran 2011 14:43 tarihinde

Re: [gmx-users] the effect of the ligand on each residue

ahmet yıldırım wrote: Dear users, I want to see the effect of the ligand on each residue using the following command: g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res Select group(s) for root mean square calculation Select a group: ? Which group should I choose? The group tha

[gmx-users] the effect of the ligand on each residue

Dear users, I want to see the effect of the ligand on each residue using the following command: g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res Select group(s) for root mean square calculation Select a group: ? Which group should I choose? Thanks in advance -- Ahmet YILDIRIM -- g

Re: [gmx-users] micelle clustering

Hi Sulatha, Did you install gromacs yourself or are you using a system wide installation? A. I installed myself In that case you go into the directory where you have put the gromacs source code and put the modified version of gmx_trjconv.c in the subdirectory src/tools. Then you go into that dir

Re: [gmx-users] micelle clustering

Dear Sulatha, You can try the command trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002 with GROMACS 4.5.4. Best regrds Grigoris --- Στις Πέμ., 30/06/11, ο/η sulatha M. S έγραψε: Από: sulatha M. S Θέμα: [gmx-users] micelle clustering Προς: "Discussion list for GROMACS users" Ημερομηνία: Πέ