[gmx-users] shear viscosity

water molecules. How can I get/derive 512 water molecules from spc216.gro? Can anyone give me some hint of this? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www

[gmx-users] Re: extreme projections

any one please help me out with this problem? 2013/7/10 Ahmet yıldırım > Dear users, > > I extracted separate extreme projections using g_anaeig. I have to make > pictures which show the difference. Can you help me, someone who makesthem > using pymolbefore > ? >

Re: [gmx-users] Figures of PCA analysis

the actual "what it means" > aspect. > > *Gesendet:* Mittwoch, 10. Juli 2013 um 14:46 Uhr > *Von:* "Ahmet yıldırım" > *An:* "Discussion list for GROMACS users" > *Betreff:* [gmx-users] Figures of PCA analysis > Dear users, > > I have

[gmx-users] extreme projections

Dear users, I extracted separate extreme projections using g_anaeig. I have to make pictures which show the difference. Can you help me, someone who makes them using pymol before? -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] Figures of PCA analysis

conformational spaces of structures??? Which one gives information about the motion of the structure? Can anyone explain to me in detail what these figure are? -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the

[gmx-users] Re: rotation of a ligand

xtc -s topol.tpr -n order.ndx -order.xvg Fatal error: grp 1 does not have same number of elements as grp 1 What should I do? 2013/5/3 Ahmet yıldırım > Dear users, > > I have a ligand bound to protein. How can I calculate how much this > ligand is rotated during the simulation time? W

[gmx-users] rotation of a ligand

Dear users, I have a ligand bound to protein. How can I calculate how much this ligand is rotated during the simulation time? Which tool should I use? g_order, g_chi, g_dih? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] g_analyze error bar

First column is time, second is rmsd value and third column is 0. average.xvg 10 0.3123 0 20 0.3256 0 30 0.3981 0 40 0.3512 0 50 0.3754 0 ... 2013/4/16 Justin Lemkul > > > > On 4/16/13 4:26 PM, Ahmet yıldırım wrote: >> >> Dear users, >> >> g_analyze -f rms

[gmx-users] g_analyze error bar

Dear users, g_analyze -f rmsd.xvg -av average.xvg -errbar stddev Unfortunately, this command didn't produce the error bar How can I obtain error bar for plotting? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

Re: [gmx-users] Re: thermal conductivity,specific heat,enthalpy

37580.html"; cP = ( - ^2)/kB T^2 (NPT sim) This formula doesn't equal to equation 13. There isnt ^2 term in equation 13. Why? Thanks in advance 2013/4/12 David van der Spoel > On 2013-04-11 22:20, Ahmet yıldırım wrote: > >> could anybody help me please? >> >

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

rce = 4.9830578e+01 2013/4/15 Justin Lemkul > > > On 4/15/13 7:22 AM, Ahmet yıldırım wrote: > >> I did as you said. I corrected number of water molecules in the topology >> by >> hand. >> >> grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o >> prote

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? 2013/4/15 Justin Lemkul > > > On 4/15/13 6:58 AM, Ahmet yıldırım wrote: > >> I have the following files in directory >> 1.tip5p.gro >> 2.topol.top >> 3.em.mdp >> >&g

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

error: No molecules were defined in the system There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım > wrote: > > > I am simulating tip

[gmx-users] Re: thermal conductivity,specific heat,enthalpy

could anybody help me please? 2013/4/11 Ahmet yıldırım > Dear users, > > I calculated diffusion constant of a substance using g_msd tool. I also > want to calculate thermal conductivity its. By the way,I did npt simulation. > > Diffusion constant=alpha > Thermal conductiv

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr Fatal error: number of coordinates in coordinate file (protein-water.gro, 37090) does not match topology (protein.top, 34530) 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 7:28 AM, Ahmet yıldırım >

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım > wrote: > > > I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from > > gromacs

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım > wrote: > > > Dear Justin, > > > > I copied to gmx.ff it. You know the tip5p shows the

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. How can you get it? 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldı

[gmx-users] thermal conductivity,specific heat,enthalpy

#Surf*SurfTen 36 Mu-X 37 Mu-Y38 Mu-Z39 T-System40 Lamb-System Firstly I calculated Entalphy (16) Afterward I calculated both Etot (7) and pV (15) Enthalpy=Etot+pV Unfortunately, I get "Enthalpy isnt equals to Etot+pV". Why? -- Ahmet Yıldırım --

[gmx-users] tip5p water model:Atomtype LP1 not found

1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] water models tip3p.gro and spce.gro

Dear users, I will run MD simulations of all water models in Gromacs. I need spce.gro and tip3p.gro files. How can I find them? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

Re: [gmx-users] RE: diffusion constant level off

st (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- gmx-users mailing listgmx-u

Re: [gmx-users] Re: diffusion constant level off

Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ 2013/3/28 Justin Lemkul > On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım > wrote: > > > Dear users, > > > > Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, &g

Re: [gmx-users] Re: diffusion constant level off

as you said, I will get only one diffusion coefficient. I want to > > calculate one diffusion coefficient for each 10 > > ns of the simulation time of 200 ns. That is, I want to get 20 diffusion > > values. > > > > 2013/3/28 David van der Spoel > > > >>

Re: [gmx-users] Re: diffusion constant level off

Dear Prof.Spoel, if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel > On 2013-03-28 10:40, Ahmet yıldırım wr

[gmx-users] Re: diffusion constant level off

Ahmet yıldırım > > Dear users, > > I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration,

[gmx-users] diffusion constant level off

of D and c? 4.) What should be "Time between restarting points in trajectory"? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mai

Re: [gmx-users] compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition

m.**vt.edu/Pages/Personal/justin< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > ==**== > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-u

Re: [gmx-users] regarding the cosine content analysis

Mon, Feb 25, 2013 at 1:23 PM, Ahmet yıldırım > wrote: > > Hi, > > > > I think my question was misunderstood. > > My question is: > > Why is second cosine content greater than the other values? > > > > Regards > > > > 2013/2/25 Thomas Evang

Re: [gmx-users] regarding the cosine content analysis

t; 0-20ns > > > 0-30ns > > > 0-40ns > > > ... > > > 0-100ns > > > > > > Until the cosine content of the first 3 principal components that > account > > > for most of the variance in the atomic fluctuation have been dropped at > >

[gmx-users] Re: regarding the cosine content analysis

Dear users, I did not get any response in my last email. Any help will be appreciated. Thanks in advance 2013/2/22 Ahmet yıldırım > Dear users, > > I performed MD simulation of 400 ns of a structure. I used the cosine > content to check whether the simulation is not converged. I u

[gmx-users] regarding the cosine content analysis

2 0.137028 3 0.00139929 4 0.00903137 5 0.0180072 6 0.0128686 7 0.00154502 8 9.71793e-05 9 0.00485945 10 0.00202377 Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] virtual sites in reference structure

Dear Tsjerk, Do the virtual sites cause incorrect calculations of SASA, RMSD or something else? Regards 2013/2/21 Tsjerk Wassenaar > Hi Ahmet, > > You can always use suitable index groups for analysis. > > Cheers, > > Tsjerk > > On Thu, Feb 21, 2013 at 7:08 AM, Ahm

Re: [gmx-users] virtual sites in reference structure

I thought the virtual sites can affect analysis.For example, dont they cause incorrect calculations of SASA, RMSD or something else? Thanks in advance 2013/2/20 Justin Lemkul > > > On 2/20/13 9:18 AM, Ahmet yıldırım wrote: > >> Dear users, >> >> I have the virtua

[gmx-users] the meaning of the dummy atom

Dear users, What is the meaning of the dummy atom in Gromacs? Regards -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

[gmx-users] virtual sites in reference structure

Dear users, I have the virtual sites in reference structure and all trajectory. When analyzing simulation, do I have to get rid of those(virtual sites)? If yes/no, why? Regards -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Re: Reference structure for PCA.

; *--- > >> >> Thanks and Regards, > >> >> Bipin Singh* > >> >> -- > >> >> gmx-users mailing listgmx-users@gromacs.org > >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >>

[gmx-users] suffice of position restraints

Dear users, I usually apply the positions restraint of 100 ps on system. Does it produce a problem to apply the positions restraint for long time (100 or 200 ps)? cant it cause strain on structure? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] activation energy

ion do you use? > > > On 01/14/2013 01:15 PM, Ahmet yıldırım wrote: > >> Dear users, >> >> Is it possible to calculate the activation energy of a structure using >> Gromacs? if OK, how? >> >> Thanks in advance >> > -- > gmx-users mailing

[gmx-users] activation energy

Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] coordinates obtained from the Automated Topology Builder

interactions, which coordinates I use? Optimised coordinates obtained from the Automated Topology Builder or original coordinates in .pdb? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the

[gmx-users] increase of temperature or pressure

temperature or pressure? What are your suggestions for the solution? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

[gmx-users] cosine content and nonconverged trajectory

Groot). What is a high cosine content? 0.2, 0.5 or 0.7 What is the value? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

Re: [gmx-users] regarding converge of system

whether or not converge of > structure/system. Why? > > 2-Radius of gyration, RMSD, rmsd matrix are used as an indicator of > convergence of the structure. are there other indicators of > convergence of the structure? > > Thanks in advance > > -- > Ahmet Yıldırım > -- >

[gmx-users] regarding converge of system

re used as an indicator of convergence of the structure. are there other indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archiv

[gmx-users] tpr file

? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list

Re: [gmx-users] Regarding RMSD analysis result

fo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.

Re: [gmx-users] Regarding RMSD analysis result

>> -- > >> Regards > >> N.NagaSundaram > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/

[gmx-users] content of secondary structure output file

in_Separator" 0 34174 131 44338 168 0 0 1 20 33184 119 63741 165 0 6 1 40 33378 121 84139 165 0 6 1 ... -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org

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

Dear users, any suggestion? Thanks in advance 2012/7/2 ahmet yıldırım > > Dear users, > > Which analysis do you suggest to examine the effect of ligand on protein? > > 1.)For quality assurance: > RMSD,RMSF and Radius of gyration for free and complex form > > 2.)For

[gmx-users] the effect of ligand on protein

eigenvectors Are these analyzes adequate? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

[gmx-users] try2

try2 -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't pos

[gmx-users] the RMSD of Bond lengths, Bond angles, Dihedrals and Impropers

create index files? Cheers -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests t

[gmx-users] renumber charge group

0.636 15.9994 14 H1TRIS H40.463 1.0080 ; 1.000 ; total charge of the molecule: 1.000 -- Ahmet Yıldırım <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] parameters of em.mdp

part of your md.mdp* nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) for energy minimization? Thanks in advance 23 Mart 2012 19:31 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear user

[gmx-users] parameters of em.mdp

ve dielectric constant of the reaction field ; VdW vdw-type= Cut-off ; twin-range cut-off with rlist where rvdw >= rlist rvdw= 1.4 ; [nm] distance for LJ cut-off ; Bonds constraints = none ; convert all bonds to constr

Re: [gmx-users] Re: Neigborsearching, Electrostatics and vdw options

I suggest you read section 4.6.3 (and probably also 4.6.2) in the > Gromacs Manual. > The Difference between rcoulomb (or rvdw) and rlist is a buffer-zone > for the fact that the > neighbor-lists are only updated every nstlist steps (often nstlist = 5). > > Oliver > > 2012

[gmx-users] Re: Neigborsearching, Electrostatics and vdw options

erspacing and rlist. Thanks in advance 21 Mart 2012 20:53 tarihinde ahmet yıldırım yazdı: > Dear users, > > I have two configuration as the following related to Neigborsearching, > Electrostatics and vdw options. I checked the literature: > Generally the rlist, rcoulomb

[gmx-users] Neigborsearching, Electrostatics and vdw options

ELECTROSTATICS AND VDW coulombtype = PME pme_order = 4 fourierspacing = 0.16 *rcoulomb = 0.9 * vdw-type = Cut-off *rvdw = 1.4* ... Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users

[gmx-users] pme note

Dear users, I get the following note: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing What should I do? Thanks in advance -- Ahmet Yıldırım

[gmx-users] one ligand in ATB

coordinates when it obtains .gro and .itp files. can I use these files obtained from ATB? If ok, doesn't the location/position of the ligand change in the enzyme? Greetings -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users P

[gmx-users] rerun problem

appended to new files (traj.xtc, ener.edr, md.log). What should I do? Cheers, -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

Re: [gmx-users] overheating problem

Hi, I put a new cooler (Thermaltake Friock) on the CPU. The problem is solved. 2012/2/4 Mark Abraham > On 4/02/2012 11:15 PM, ahmet yıldırım wrote: > > Hi, > The problem might caused by X58 chipset. > Now I am using ubuntu. Which operating system do you recommend? > > >

Re: [gmx-users] overheating problem

Hi, The problem might caused by X58 chipset. Now I am using ubuntu. Which operating system do you recommend? 2012/2/4 David van der Spoel > On 2012-02-03 23:49, ahmet yıldırım wrote: > >> Dear Mark, >> >> >> Believe me, I tried all methods that you said but unfo

Re: [gmx-users] overheating problem

Dear Mark, Believe me, I tried all methods that you said but unfortunately the result doesnt change :( 2012/2/4 Mark Abraham > On 4/02/2012 8:24 AM, ahmet yıldırım wrote: > > Dear users, > > I am using ubuntu 11.1 (64 bit). The Ubuntu normally runs when I dont run > the Gr

Re: [gmx-users] Error in installation

rs mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www

Re: [gmx-users] multi file input for index files

ndon SW7 2AZ > E: j.marzine...@imperial.ac.uk > M: +44(0)7411 640 552 > -- > *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of ahmet yıldırım [ahmedo...@gmail.com] > *Sent:* Tuesday, January 10, 2012 8:13 AM > *To:* Discussion list for GROMACS user

Re: [gmx-users] multi file input for index files

Hi, But I want to calculate the hydrogen bonds between A and B groups. If I do as you said, I will have calculated intra hydrogen bonds of a group AB (merged A and B). 2012/1/10 Mark Abraham > On 10/01/2012 7:13 PM, ahmet yıldırım wrote: > >> Dear users, >> >> I cre

[gmx-users] multi file input for index files

. "Gromacs tools do not support multi file input for index files" from http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. Is this correct? If no, what should I do? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] calculation time

steps, 3.0 ps. 2011/10/19 Mark Abraham > On 19/10/2011 5:04 PM, ahmet yıldırım wrote: > > For example; > > grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o run.tpr > mdrun -v -deffnm run > > ... > 1500 steps, 3.0 ps. > step 100, will finish S

Re: [gmx-users] calculation time

gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Mark Abraham > Sent: Wednesday, 19 October 2011 3:08 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] calculation time > > On 19/10/2011 5:26 AM, ahmet yıldırım wrote: > > Dear users, &

[gmx-users] calculation time

Dear users, Sometimes, in the end ( in production simulation), Gromacs doesn't show calculation/finish time on screen, why? How can we show it? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sear

Re: [gmx-users] RMSD bonds and angles

No, it calculates with respect to the positions atom. but I want to calculate the RMSD bonds (A˚ ) and RMSD angles (o). 2011/10/4 Mark Abraham > On 4/10/2011 7:05 PM, ahmet yıldırım wrote: > > any hints? :( > > > You didn't find something useful in the section t

Re: [gmx-users] RMSD bonds and angles

any hints? :( 03 Ekim 2011 22:32 tarihinde ahmet yıldırım yazdı: > I look at chapter 8 but I didnt found that I want. can you give a hint? > Thanks > > > 2011/10/3 Mark Abraham > >> On 3/10/2011 10:29 PM, ahmet yıldırım wrote: >> >>> Dear users, >&g

[gmx-users] heteroatom not to be a ligand

Dear users, I have a xxx .pdb including enzyme+X. But X is a cryoprotectant, that is heteroatom, it is not a ligand. I think I shouldn't use a way as Justin tutorial 5. Because X is not a ligand. what should I do? Thanks -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] RMSD bonds and angles

I look at chapter 8 but I didnt found that I want. can you give a hint? Thanks 2011/10/3 Mark Abraham > On 3/10/2011 10:29 PM, ahmet yıldırım wrote: > >> Dear users, >> >> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? >> > > Please start yo

[gmx-users] RMSD bonds and angles

Dear users, How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

Re: [gmx-users] if PRODRG calculate incorrectly

using another program? I was obtaining .gro and .itp files using PRODRG but PRODRG is giving improper results/output. best regards 2011/9/17 Mark Abraham > On 17/09/2011 11:28 PM, ahmet yıldırım wrote: > >> Dear Tsjerk and Justin, >> >> Thanks for your reply. I will

Re: [gmx-users] meaning of minus potential and buried surface area

Dear Justin, If possible, can you some explain "net attraction"? Best regards 2011/9/22 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> >> 1.) During the simulation the mean potential energy is minus (-) value. >> What do

Re: [gmx-users] what difference between RMSF and RMDEV

of N atom:[(x1+x2+x3)/3, (y1+y2+y3)/3, (z1+z2+z3)/3]. isnt it? x y z 6 4 3 3.) This "The reference structure used to remove translational and rotational degrees of freedom" is RMSD??? 2011/9/21 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> &

[gmx-users] meaning of minus potential and buried surface area

Dear users, 1.) During the simulation the mean potential energy is minus (-) value. What does this mean? Why minus? 2.) let's say, Interface/Buried Surace Area (ISA) between protein and ligand was calculated and hydrophobic ISA obtained greater than hydrophilic ISA. What does this mean? No one is

[gmx-users] what difference between RMSF and RMDEV

Dear users, g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res With the option -od the root mean square deviation with respect to the reference structure is calculated. Then, RMSDEV is the RMSD per residue (the root mean square deviation with respect to the reference structure is calcul

Re: [gmx-users] if PRODRG calculate incorrectly

Dear Tsjerk and Justin, Thanks for your reply. I will contact the PRODRG developers. can you suggest anyway/anytool for generating ligand coordinates/topologies? Thanks in advance 17 Eylül 2011 15:58 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear

[gmx-users] if PRODRG calculate incorrectly

Dear users, I have a problem related to PRODRG. Chirality:NO Full charges: YES Energy minimization: NO *İnput file name:TRS.pdb* HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99 C ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45-81 C HETATM 1804 C1 TRS B 232

Re: [gmx-users] residue SASA

There are hydrophilic and hydrophobic SASA values versus simulation time in the output file (area.xvg). I want to hydrophilic and hydrophobic SASA values versus residue. 2011/7/7 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> >> I want to calcul

[gmx-users] residue SASA

Dear users, I want to calculate hydrophilic and hyrophobic SASA value of each residue in protein. I used a command as the following: g_sas -f run.xtc -s run.tpr -or protein_protein.xvg Select a group for calculation of surface and a group for output select a group: 1 (protein) select a group: 2 (

Re: [gmx-users] g_sas calculation

)=(protein)+(ligand)-(protein_ligand)* Thanks 2011/7/3 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> >> I want to compute SASA between protein and ligand. >> *1.)* >> protein and ligand are merged by make_ndx >> g_sas -f run.xtc -s run

[gmx-users] g_sas calculation

Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein+ligand) select a group:

Re: [gmx-users] g_mindist

Dear Justin, can you suggest me published paper related to about hydrophobic and hydrophilic contacts? 03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear Justin, >> >> You said before "you can obtain some i

[gmx-users] g_mindist

Dear Justin, You said before "you can obtain some idea by using g_mindist to calculate hydrophobic and hydrophilic contacts between the protein and ligand". That is, I can explore whether there is hydrophobic or hydrophilic feature of ligand using g_mindist tool. is this correct? I did the calcul

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

0 Haziran 2011 14:43 tarihinde Justin A. Lemkul yazdı: > > > 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 >

[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] protein-ligand interaction

228 0.1034 229 0.1161 230 0.1206 29 Mayıs 2011 19:28 tarihinde ahmet yıldırım yazdı: > Dear Justin, > > I used -res flag with the following command but I get pairs of values in > the output files. is there any mistake related with the command I used? > g_rmsf -s run.t

Re: [gmx-users] protein-ligand interaction

Dear Justin, I used -res flag with the following command but I get pairs of values in the output files. is there any mistake related with the command I used? g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res 2011/5/29 > Quoting ahmet y?ld?r?m : > > Dear Justin, >> >> You said " Y

Re: [gmx-users] protein-ligand interaction

Dear Justin, You said " You can get a per-residue RMSD by using g_rmsf -od to see the effect of the ligand on each residue." 1. Can you explain the difference between what goes into the -o file, and what goes into the -od file? 2. How should I create a index file to see the effect of the ligand o

[gmx-users] protein-ligand interaction

Dear users, I want to investigate *Ligand effect *on the protein . To investigation the interaction of protein-ligand: *RMSD calculations:* 1. a) RMSD of Backbone b) RMSD of Backbone+ligand 2. a) RMSD of Protein b) RMSD of Protein+ligand 3. a) RMSD of Protein-H b) RMSD of Protein-H+ligand Which on

[gmx-users] NPT and NVT ensembles

Dear Justin, In the first tutorial You said "After we arrive at the correct temperature (based on kinetic energies), we will apply pressure to the system until it reaches the proper density." That is, you apply each NVT and NPT ensembles when you did the position restraints. Would not it only be s

Re: [gmx-users] index file

oup will contain atoms that are common to both LIGA > > and LIGB. If they are distinct entities, the group will be empty. > Logical > > or (|) says merge the two different groups to create one unified group. > > Ooops > > > > > > -Justin > > > >&

[gmx-users] index file

Dear users, I have two ligands. I created a special index group that merges the protein, LiGA and LİGB. I have the pr.mdp file as the following: ... energygrps = ProteinLİGA_LİGB tc-grps = Protein_LİGA_LİGBWater_and_ions ... grompp -f pr.mdp -p topol.top -c em.gro -n index.n

Re: [gmx-users] principal moments of ellipsoid

Hi, BioVEC is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to berendered as ellipsoids. http://www.phas.ubc.ca/~steve/BioVEC/BioVECindex.html 2011/5/10 Mark Abraham > On 10/05/2011 8:23 PM, lammps lammps wrote: > >> Hi, >> I want to study the

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